Class picard.cmdline.CommandLineParserTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testAddToDefaultValuesListOption | 0.001s | passed |
| testBadEnumValue | 0.028s | passed |
| testBadValue | 0.005s | passed |
| testClearDefaultValuesFromListOption | 0s | passed |
| testClearDefaultValuesFromListOptionAndAddNew | 0s | passed |
| testCollectionThatCannotBeAutoInitialized | 0.001s | passed |
| testDefault | 0.001s | passed |
| testDynamicNestedOptions | 0.010s | passed |
| testDynamicPropagation | 0.009s | passed |
| testForIdenticalShortName | 0s | passed |
| testHTMLConverter[0](hello, hello) | 0.001s | passed |
| testHTMLConverter[10](hi</li>bye, hi bye) | 0.001s | passed |
| testHTMLConverter[11](Using read outputs from high throughput sequencing (HTS) technologies, this tool provides metrics regarding the quality of read alignments to a reference sequence, as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters (Illumina).<h4>Usage example:</h4><pre> java -jar picard.jar CollectAlignmentSummaryMetrics \<br /> R=reference_sequence.fasta \<br /> I=input.bam \<br /> O=output.txt</pre>Please see <a href='http://broadinstitute.github.io/picard/picard-metric-definitions.html#AlignmentSummaryMetrics'>the AlignmentSummaryMetrics documentation</a> for detailed explanations of each metric. <br /> <br />Additional information about Illumina's quality filters can be found in the following documents on the Illumina website:<ul><li><a href="http://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/hiseq-x-percent-pf-technical-note-770-2014-043.pdf">hiseq-x-percent-pf-technical-note</a></li><li><a href="http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseqx/hiseq-x-system-guide-15050091-d.pdf">hiseq-x-system-guide</a></li></ul><hr />, Using read outputs from high throughput sequencing (HTS) technologies, this tool provides metrics regarding the quality of read alignments to a reference sequence, as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters (Illumina). Usage example: java -jar picard.jar CollectAlignmentSummaryMetrics \ R=reference_sequence.fasta \ I=input.bam \ O=output.txt Please see the AlignmentSummaryMetrics documentation (http://broadinstitute.github.io/picard/picard-metric-definitions.html#AlignmentSummaryMetrics) for detailed explanations of each metric. Additional information about Illumina's quality filters can be found in the following documents on the Illumina website: - hiseq-x-percent-pf-technical-note (http://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/hiseq-x-percent-pf-technical-note-770-2014-043.pdf) - hiseq-x-system-guide (http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseqx/hiseq-x-system-guide-15050091-d.pdf) ) | 0s | passed |
| testHTMLConverter[1](, ) | 0s | passed |
| testHTMLConverter[2](hi</th>bye, hi bye) | 0s | passed |
| testHTMLConverter[3](hi<th>bye, hibye) | 0s | passed |
| testHTMLConverter[4](hi<li>bye, hi - bye) | 0s | passed |
| testHTMLConverter[5](hi<NOT_A_REAL_TAG>bye, hibye) | 0.001s | passed |
| testHTMLConverter[6](</h4><pre>, ) | 0s | passed |
| testHTMLConverter[7](<a href="http://go.here.org"> string</ a >, string (http://go.here.org)) | 0s | passed |
| testHTMLConverter[8](<a href="http://go.here.org" > string</ a>, string (http://go.here.org)) | 0s | passed |
| testHTMLConverter[9](< a href="http://go.here.org"> string<a />, string (http://go.here.org)) | 0s | passed |
| testHtmlUnescape[0](<, <) | 0s | passed |
| testHtmlUnescape[1](x<y, x<y) | 0s | passed |
| testHtmlUnescape[2](x<y<z, x<y<z) | 0s | passed |
| testHtmlUnescape[3]( , <p>) | 0s | passed |
| testHtmlUnescape[4](<html> x<y </html> y< <strong> x </strong>, <html> x<y </html> y< <strong> x </strong>) | 0s | passed |
| testMissingRequiredArgument | 0.009s | passed |
| testMutex[0](pass, [Ljava.lang.String;@26f3c4a8, true) | 0.001s | passed |
| testMutex[1](no args, [Ljava.lang.String;@f1bcec, false) | 0.007s | passed |
| testMutex[2](1 of group required, [Ljava.lang.String;@1e1aab86, false) | 0.002s | passed |
| testMutex[3](mutex, [Ljava.lang.String;@30ef5531, false) | 0.002s | passed |
| testMutex[4](mega mutex, [Ljava.lang.String;@3c4ce719, false) | 0.002s | passed |
| testNonAsciiAssertion | 0.001s | passed |
| testNonAsciiConverted | 0.009s | passed |
| testNotEnoughOfListOption | 0.002s | passed |
| testNotEnoughPositional | 0.002s | passed |
| testNullValue | 0.007s | passed |
| testOptionDefinitionCaseClash | 0s | passed |
| testOptionUseCaseClash | 0.003s | passed |
| testOptionsFile | 0.002s | passed |
| testOptionsFileWithDisallowedOverride | 0.006s | passed |
| testOveriddenOptions | 0s | passed |
| testPositive | 0.001s | passed |
| testPositiveTerminalEqualSign | 0s | passed |
| testPositiveWithSpaces | 0.001s | passed |
| testPositiveWithoutPositional | 0s | passed |
| testStaticNestedNegative | 0.004s | passed |
| testStaticNestedOptions | 0.005s | passed |
| testStaticPropagation | 0.007s | passed |
| testStaticPropagationNegative | 0.003s | passed |
| testTooManyListOption | 0.002s | passed |
| testTooManyPositional | 0.001s | passed |
| testUnexpectedPositional | 0.002s | passed |
| testUninitializedCollections | 0s | passed |
| testUsage | 0.002s | passed |
| testUsageWithDefault | 0.002s | passed |
| testUsageWithoutPositional | 0.002s | passed |
| testUsageWithoutPositionalWithDefault | 0.002s | passed |
Standard output
picard.cmdline.CommandLineParserTest$ClpOptionsWithNested AN_INT=123 A_STRING=aString VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json CLP_NESTED.VERBOSITY=INFO CLP_NESTED.QUIET=false CLP_NESTED.VALIDATION_STRINGENCY=STRICT CLP_NESTED.COMPRESSION_LEVEL=5 CLP_NESTED.MAX_RECORDS_IN_RAM=1000 CLP_NESTED.CREATE_INDEX=false CLP_NESTED.CREATE_MD5_FILE=false CLP_NESTED.GA4GH_CLIENT_SECRETS=client_secrets.json CLP_NESTED.FROB_NESTED.FROBNICATION_THRESHOLD=-1000 CLP_NESTED.FROB_NESTED.FROBNICATION_FLAVOR=BAZ CLP_NESTED.FROB_NESTED.SHMIGGLE_TYPE=[innershmiggle1, skeezwitz] CLP_NESTED.FROB_NESTED.TRUTHINESS=false FRAB.FROBNICATION_THRESHOLD=456 FRAB.FROBNICATION_FLAVOR=FOO FRAB.SHMIGGLE_TYPE=[shmiggle1] FRAB.TRUTHINESS=true
picard.cmdline.CommandLineParserTest$DynamicPropagationParent STRING3=String3Parent STRING5=String5Parent COLLECTION=[CollectionParent] STRING1=String1ParentDefault STRING2=String2ParentDefault STRING4=String4ParentDefault VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json CHILD.STRING4=String4Child CHILD.STRING5=String5Child CHILD.STRING2=String2ChildDefault CHILD.STRING3=String3ChildDefault
picard.cmdline.CommandLineParserTest$OptionsWithNested AN_INT=123 A_STRING=outerString
USAGE: OptionsWithNested [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithNested
Class with nested option
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
AN_INT=Integer Required.
A_STRING=String Required.
FROB.FROBNICATION_THRESHOLD=Integer
FROB.T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROB.FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
FROB.SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
FROB.TRUTHINESS=Boolean Required. Possible values: {true, false}
NESTED.FROB.FROBNICATION_THRESHOLD=Integer
NESTED.FROB.T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
NESTED.FROB.FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
NESTED.FROB.SHMIGGLE_TYPE=String
Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
NESTED.FROB.TRUTHINESS=BooleanRequired. Possible values: {true, false}
<h3 id="testStaticNestedOptions">testStaticNestedOptions</h3>
<section>
<p>Class with nested option</p>
<table>
<tr><th>Option</th><th>Description</th></tr>
<tr><td>AN_INT (Integer)</td><td>Required. </td></tr>
<tr><td>A_STRING (String)</td><td>Required. </td></tr>
<tr><td>FROB.FROBNICATION_THRESHOLD (Integer)</td><td>Frobnication threshold setting. Default value: 20. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>FROB.FROBNICATION_FLAVOR (FrobnicationFlavor)</td><td>Required. Possible values: {FOO, BAR, BAZ} </td></tr>
<tr><td>FROB.SHMIGGLE_TYPE (String)</td><td>Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 times. </td></tr>
<tr><td>FROB.TRUTHINESS (Boolean)</td><td>Required. Possible values: {true, false} </td></tr>
<tr><td>NESTED.FROB.FROBNICATION_THRESHOLD (Integer)</td><td>Frobnication threshold setting. Default value: 20. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>NESTED.FROB.FROBNICATION_FLAVOR (FrobnicationFlavor)</td><td>Required. Possible values: {FOO, BAR, BAZ} </td></tr>
<tr><td>NESTED.FROB.SHMIGGLE_TYPE (String)</td><td>Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 times. </td></tr>
<tr><td>NESTED.FROB.TRUTHINESS (Boolean)</td><td>Required. Possible values: {true, false} </td></tr>
</table>
</section>
picard.cmdline.CommandLineParserTest$OptionsWithNested AN_INT=123 A_STRING=outerString FROB.FROBNICATION_FLAVOR=BAR FROB.SHMIGGLE_TYPE=[shmiggle1, shmiggle2] FROB.TRUTHINESS=true FROB.FROBNICATION_THRESHOLD=20 NESTED.FROB.FROBNICATION_THRESHOLD=10 NESTED.FROB.FROBNICATION_FLAVOR=BAZ NESTED.FROB.SHMIGGLE_TYPE=[inner1, inner2, inner3] NESTED.FROB.TRUTHINESS=false
USAGE: StaticPropagationParent [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#StaticPropagationParent
Usage: program [options...]
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
STRING1=String Default value: String1ParentDefault. This option can be set to 'null' to clear the
default value.
STRING2=String Default value: String2ParentDefault. This option can be set to 'null' to clear the
default value.
STRING3=String Default value: String3ParentDefault. This option can be set to 'null' to clear the
default value.
STRING4=String Default value: String4ParentDefault. This option can be set to 'null' to clear the
default value.
STRING5=String Required.
COLLECTION=String Default value: null. This option may be specified 0 or more times.
CHILD.STRING1=String Required.
CHILD.STRING2=String Default value: String2ChildDefault. This option can be set to 'null' to clear the default
value.
CHILD.STRING3=String Default value: String3ChildDefault. This option can be set to 'null' to clear the default
value.
CHILD.STRING4=String Required.
CHILD.STRING5=String Required.
CHILD.COLLECTION=String Default value: null. This option may be specified 0 or more times.
<h3 id="testStaticPropagation">testStaticPropagation</h3>
<section>
<p>Usage: program [options...]
</p>
<table>
<tr><th>Option</th><th>Description</th></tr>
<tr><td>STRING1 (String)</td><td>Default value: String1ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>STRING2 (String)</td><td>Default value: String2ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>STRING3 (String)</td><td>Default value: String3ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>STRING4 (String)</td><td>Default value: String4ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>STRING5 (String)</td><td>Required. </td></tr>
<tr><td>COLLECTION (String)</td><td>Default value: null. This option may be specified 0 or more times. </td></tr>
<tr><td>CHILD.STRING1 (String)</td><td>Required. </td></tr>
<tr><td>CHILD.STRING2 (String)</td><td>Default value: String2ChildDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>CHILD.STRING3 (String)</td><td>Default value: String3ChildDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>CHILD.STRING4 (String)</td><td>Required. </td></tr>
<tr><td>CHILD.STRING5 (String)</td><td>Required. </td></tr>
<tr><td>CHILD.COLLECTION (String)</td><td>Default value: null. This option may be specified 0 or more times. </td></tr>
</table>
</section>
picard.cmdline.CommandLineParserTest$StaticPropagationParent STRING3=String3Parent STRING5=String5Parent COLLECTION=[CollectionParent] STRING1=String1ParentDefault STRING2=String2ParentDefault STRING4=String4ParentDefault CHILD.STRING4=String4Child CHILD.STRING5=String5Child CHILD.STRING2=String2ChildDefault CHILD.STRING3=String3ChildDefault
USAGE: NegativePropagationParent [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#NegativePropagationParent
Usage: program [options...]
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
STRING1=Integer Default value: 1. This option can be set to 'null' to clear the default value.
COLLECTION=String Default value: null. This option may be specified 0 or more times.
CHILD.STRING1=String Required.
CHILD.STRING2=String Default value: String2ChildDefault. This option can be set to 'null' to clear the default
value.
CHILD.STRING3=String Default value: String3ChildDefault. This option can be set to 'null' to clear the default
value.
CHILD.STRING4=String Required.
CHILD.STRING5=String Required.
CHILD.COLLECTION=String Default value: null. This option may be specified 0 or more times.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
USAGE: OptionsWithoutPositional [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithoutPositional
Usage: framistat [options]
Compute the plebnick of the freebozzle.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
USAGE: OptionsWithoutPositional [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithoutPositional
Usage: framistat [options]
Compute the plebnick of the freebozzle.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
Standard error
ERROR: 'HiMom' is not a valid value for FrobnicationFlavor.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
ERROR: Problem constructing Integer from the string 'ABC'.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
USAGE: ClpOptionsWithNested [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#ClpOptionsWithNested
Class with nested options.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
AN_INT=Integer Required.
A_STRING=String Required.
CLP_NESTED.FROB_NESTED.FROBNICATION_THRESHOLD=Integer
CLP_NESTED.FROB_NESTED.T=Integer
Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
CLP_NESTED.FROB_NESTED.FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
CLP_NESTED.FROB_NESTED.SHMIGGLE_TYPE=String
Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
CLP_NESTED.FROB_NESTED.TRUTHINESS=Boolean
Required. Possible values: {true, false}
<h3 id="ClpOptionsWithNested">ClpOptionsWithNested</h3>
<section>
<p>Class with nested options.</p>
<table>
<tr><th>Option</th><th>Description</th></tr>
<tr><td>AN_INT (Integer)</td><td>Default value: 123. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>A_STRING (String)</td><td>Default value: aString. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>CLP_NESTED.FROB_NESTED.FROBNICATION_THRESHOLD (Integer)</td><td>Frobnication threshold setting. Default value: -1000. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>CLP_NESTED.FROB_NESTED.FROBNICATION_FLAVOR (FrobnicationFlavor)</td><td>Default value: BAZ. This option can be set to 'null' to clear the default value. Possible values: {FOO, BAR, BAZ} </td></tr>
<tr><td>CLP_NESTED.FROB_NESTED.SHMIGGLE_TYPE (String)</td><td>Allowed shmiggle types. Default value: [innershmiggle1, skeezwitz]. This option can be set to 'null' to clear the default value. This option may be specified between 1 and 3 times. This option can be set to 'null' to clear the default list. </td></tr>
<tr><td>CLP_NESTED.FROB_NESTED.TRUTHINESS (Boolean)</td><td>Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} </td></tr>
</table>
</section>
USAGE: DynamicPropagationParent [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#DynamicPropagationParent
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
STRING1=String Default value: String1ParentDefault. This option can be set to 'null' to clear the
default value.
STRING2=String Default value: String2ParentDefault. This option can be set to 'null' to clear the
default value.
STRING3=String Default value: String3ParentDefault. This option can be set to 'null' to clear the
default value.
STRING4=String Default value: String4ParentDefault. This option can be set to 'null' to clear the
default value.
STRING5=String Required.
COLLECTION=String Default value: null. This option may be specified 0 or more times.
CHILD.STRING1=String Required.
CHILD.STRING2=String Default value: String2ChildDefault. This option can be set to 'null' to clear the default
value.
CHILD.STRING3=String Default value: String3ChildDefault. This option can be set to 'null' to clear the default
value.
CHILD.STRING4=String Required.
CHILD.STRING5=String Required.
CHILD.COLLECTION=String Default value: null. This option may be specified 0 or more times.
<h3 id="DynamicPropagationParent">DynamicPropagationParent</h3>
<section>
<p></p>
<table>
<tr><th>Option</th><th>Description</th></tr>
<tr><td>STRING1 (String)</td><td>Default value: String1ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>STRING2 (String)</td><td>Default value: String2ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>STRING3 (String)</td><td>Default value: String3Parent. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>STRING4 (String)</td><td>Default value: String4ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>STRING5 (String)</td><td>Default value: String5Parent. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>COLLECTION (String)</td><td>Default value: [CollectionParent]. This option can be set to 'null' to clear the default value. This option may be specified 0 or more times. This option can be set to 'null' to clear the default list. </td></tr>
<tr><td>CHILD.STRING1 (String)</td><td>Default value: String1ParentDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>CHILD.STRING2 (String)</td><td>Default value: String2ChildDefault. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>CHILD.STRING3 (String)</td><td>Default value: String3Parent. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>CHILD.STRING4 (String)</td><td>Default value: String4Child. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>CHILD.STRING5 (String)</td><td>Default value: String5Child. This option can be set to 'null' to clear the default value. </td></tr>
<tr><td>CHILD.COLLECTION (String)</td><td>Default value: null. This option may be specified 0 or more times. </td></tr>
</table>
</section>
ERROR: Option 'FROBNICATION_FLAVOR' is required.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
ERROR: Option 'A' is required unless any of [Y, Z, M, N] are specified.
USAGE: MutexOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#MutexOptions
Usage: program [options...]
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
A=String Required. Cannot be used in conjuction with option(s) Y Z M N
B=String Required. Cannot be used in conjuction with option(s) Y Z M N
M=String Required. Cannot be used in conjuction with option(s) A B Y Z
N=String Required. Cannot be used in conjuction with option(s) A B Y Z
Y=String Required. Cannot be used in conjuction with option(s) A B M N
Z=String Required. Cannot be used in conjuction with option(s) A B M N
ERROR: Option 'B' is required unless any of [Y, Z, M, N] are specified.
USAGE: MutexOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#MutexOptions
Usage: program [options...]
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
A=String Required. Cannot be used in conjuction with option(s) Y Z M N
B=String Required. Cannot be used in conjuction with option(s) Y Z M N
M=String Required. Cannot be used in conjuction with option(s) A B Y Z
N=String Required. Cannot be used in conjuction with option(s) A B Y Z
Y=String Required. Cannot be used in conjuction with option(s) A B M N
Z=String Required. Cannot be used in conjuction with option(s) A B M N
ERROR: Option 'A' cannot be used in conjunction with option(s) Y
USAGE: MutexOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#MutexOptions
Usage: program [options...]
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
A=String Required. Cannot be used in conjuction with option(s) Y Z M N
B=String Required. Cannot be used in conjuction with option(s) Y Z M N
M=String Required. Cannot be used in conjuction with option(s) A B Y Z
N=String Required. Cannot be used in conjuction with option(s) A B Y Z
Y=String Required. Cannot be used in conjuction with option(s) A B M N
Z=String Required. Cannot be used in conjuction with option(s) A B M N
ERROR: Option 'A' cannot be used in conjunction with option(s) Y Z M N
USAGE: MutexOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#MutexOptions
Usage: program [options...]
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
A=String Required. Cannot be used in conjuction with option(s) Y Z M N
B=String Required. Cannot be used in conjuction with option(s) Y Z M N
M=String Required. Cannot be used in conjuction with option(s) A B Y Z
N=String Required. Cannot be used in conjuction with option(s) A B Y Z
Y=String Required. Cannot be used in conjuction with option(s) A B M N
Z=String Required. Cannot be used in conjuction with option(s) A B M N
ERROR: Option 'SHMIGGLE_TYPE' must be specified at least 1 times.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
ERROR: At least 2 positional arguments must be specified.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'.
USAGE: FrobnicateOptionsWithNullList [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptionsWithNullList
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Required.
FROBNICATION_FLAVOR=FrobnicationFlavor
Default value: BAR. This option can be set to 'null' to clear the default value. Possible
values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than
3 times.
TRUTHINESS=Boolean Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'.
USAGE: FrobnicateOptionsWithNullList [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptionsWithNullList
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Required.
FROBNICATION_FLAVOR=FrobnicationFlavor
Default value: BAR. This option can be set to 'null' to clear the default value. Possible
values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than
3 times.
TRUTHINESS=Boolean Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
ERROR: Option 'FROBNICATION_FLAVOR' cannot be specified more than once.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
ERROR: Option 'T' cannot be specified more than once.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
ERROR: Option 'FROB.FROBNICATION_FLAVOR' is required.
ERROR: Option 'NESTED.FROB.FROBNICATION_FLAVOR' is required.
USAGE: OptionsWithNested [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithNested
Class with nested option
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
AN_INT=Integer Required.
A_STRING=String Required.
FROB.FROBNICATION_THRESHOLD=Integer
FROB.T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROB.FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
FROB.SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
FROB.TRUTHINESS=Boolean Required. Possible values: {true, false}
NESTED.FROB.FROBNICATION_THRESHOLD=Integer
NESTED.FROB.T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
NESTED.FROB.FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
NESTED.FROB.SHMIGGLE_TYPE=String
Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
NESTED.FROB.TRUTHINESS=BooleanRequired. Possible values: {true, false}
ERROR: Option 'SHMIGGLE_TYPE' cannot be used more than 3 times.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
ERROR: No more than 2 positional arguments may be specified on the command line.
USAGE: FrobnicateOptions [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FrobnicateOptions
Usage: frobnicate [options] input-file output-file
Read input-file, frobnicate it, and write frobnicated results to output-file
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}
ERROR: Invalid argument 'positional'.
USAGE: OptionsWithoutPositional [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#OptionsWithoutPositional
Usage: framistat [options]
Compute the plebnick of the freebozzle.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
FROBNICATION_THRESHOLD=Integer
T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to
clear the default value.
FROBNICATION_FLAVOR=FrobnicationFlavor
Required. Possible values: {FOO, BAR, BAZ}
SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and
3 times.
TRUTHINESS=Boolean Required. Possible values: {true, false}