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1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="1.106.0">
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2 <description>Collect RNA-Seq Metrics</description>
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3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
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4 <command interpreter="python">
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5 picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
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6 -n "${out_prefix}" --tmpdir "${__new_file_path__}" --assumesorted ${ASSUME_SORTED}
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7 --refflat ${REF_FLAT}
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8 #if $identify_ribosomal.opt == "yes"
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9 --ribosomalintervals ${identify_ribosomal.RIBOSOMAL_INTERVALS}
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10 #end if
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11 --malevel "${malevel}"
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12 --minlength ${MINIMUM_LENGTH}
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13 --strandspecificity ${STRAND_SPECIFICITY}
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14 --rrnafragmentpercentage ${RRNA_FRAGMENT_PERCENTAGE}
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15 #for $i in $IGNORE_SEQUENCES
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16 --ignoreseq "${i.IGNORE_SEQUENCE}"
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17 #end for
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18 -j "\$JAVA_JAR_PATH/CollectRnaSeqMetrics.jar"
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19 </command>
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20
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21 <stdio>
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22 <exit_code range="0" level="warning" description="Tool finished correctly" />
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23 </stdio>
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24
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25 <inputs>
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26 <param format="sam" name="input_file" type="data" label="Input SAM file." help="" />
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27
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28 <param format="data" name="REF_FLAT" type="data" label="Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required." help="" />
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29
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30 <conditional name="identify_ribosomal">
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31 <param name="opt" type="select" label="Identify ribosomal bases" help="If 'no' is selected, no bases will be identified as being ribosomal.">
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32 <option value="no">no</option>
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33 <option value="yes">yes</option>
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34 </param>
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35 <when value="no" />
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36 <when value="yes">
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37 <param format="data" name="RIBOSOMAL_INTERVALS" type="data" label="Location of rRNA sequences in genome, in interval_list format. If not specified no bases will be identified as being ribosomal. Format described here: http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html Default value: null." help="" />
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38 </when>
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39 </conditional>
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40
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41 <param name="STRAND_SPECIFICITY" type="select" label="For strand-specific library prep." help="For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand. {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}">
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42 <option value="NONE" selected="True">None</option>
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43 <option value="FIRST_READ_TRANSCRIPTION_STRAND">FIRST_READ_TRANSCRIPTION_STRAND</option>
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44 <option value="SECOND_READ_TRANSCRIPTION_STRAND">SECOND_READ_TRANSCRIPTION_STRAND</option>
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45 </param>
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46
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47 <param name="MINIMUM_LENGTH" type="text" value="500" label="When calculating coverage based values (e.g. CV of coverage) only use transcripts of this length or greater." help="" />
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48
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49 <repeat name="IGNORE_SEQUENCES" title="Ignore Sequences">
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50 <param name="IGNORE_SEQUENCE" label="Ignore Sequence" type="text" help="If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases." />
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51 </repeat>
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52
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53 <param name="RRNA_FRAGMENT_PERCENTAGE" type="text" value="0.8" label="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair by this must in order to be considered rRNA." help="" />
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54
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55 <param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level"
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56 help="Level(s) at which metrics will be accumulated">
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57 <option value="ALL_READS" selected="true">All reads (default)</option>
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58 <option value="SAMPLE" default="true">Sample</option>
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59 <option value="LIBRARY" default="true">Library</option>
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60 <option value="READ_GROUP" default="true">Read group</option>
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61 </param>
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62
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63 <param checked="True" truevalue="true" falsevalue="false" name="ASSUME_SORTED" type="boolean" label="If true (default), then the sort order in the header file will be ignored." />
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64 </inputs>
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65 <outputs>
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66 <data format="html" name="html_file" label="${out_prefix}.html"/>
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67 </outputs>
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68 <tests>
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69 <test>
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70
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71 </test>
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72 </tests>
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73 <help>
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74 Picard documentation says:
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75
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76
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77 CollectRnaSeqMetrics
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78
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79 Documentation: http://picard.sourceforge.net/command-line-overview.shtml#CollectRnaSeqMetrics
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80 Program to collect metrics about the alignment of RNA to various functional classes of loci in the genome: coding, intronic, UTR, intergenic, ribosomal. Also determines strand-specificity for strand-specific libraries.
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81 Option Description
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82 REF_FLAT=File Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required.
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83 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases will be identified as being ribosomal. Format described here: http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html Default value: null.
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84 STRAND_SPECIFICITY=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand. Required. Possible values: {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}
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85 MINIMUM_LENGTH=Integer When calculating coverage based values (e.g. CV of coverage) only use transcripts of this length or greater. Default value: 500. This option can be set to 'null' to clear the default value.
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86 CHART_OUTPUT=File The PDF file to write out a plot of normalized position vs. coverage. Default value: null.
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87 IGNORE_SEQUENCE=String If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases. These reads are not counted as This option may be specified 0 or more times.
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88 RRNA_FRAGMENT_PERCENTAGE=Double This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair by this must in order to be considered rRNA. Default value: 0.8. This option can be set to 'null' to clear the default value.
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89 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list.
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90 INPUT=File Input SAM or BAM file. Required.
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91 OUTPUT=File File to write the output to. Required.
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92 REFERENCE_SEQUENCE=File Reference sequence fasta Default value: null.
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93 ASSUME_SORTED=Boolean If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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94 STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value.
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95
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96
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97 </help>
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98 </tool>
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