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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 <param name="out_prefix" value="RNA-Seq Metrics" type="text"
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28 label="Title for the output file" help="Use this remind you what the job was for." size="80" />
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29
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30 <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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31
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32 <conditional name="identify_ribosomal">
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33 <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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34 <option value="no">no</option>
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35 <option value="yes">yes</option>
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36 </param>
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37 <when value="no" />
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38 <when value="yes">
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39 <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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40 </when>
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41 </conditional>
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42
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43 <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.">
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44 <option value="NONE" selected="True">None</option>
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45 <option value="FIRST_READ_TRANSCRIPTION_STRAND">FIRST_READ_TRANSCRIPTION_STRAND</option>
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46 <option value="SECOND_READ_TRANSCRIPTION_STRAND">SECOND_READ_TRANSCRIPTION_STRAND</option>
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47 </param>
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48
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49 <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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50
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51 <repeat name="IGNORE_SEQUENCES" title="Ignore Sequences">
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52 <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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53 </repeat>
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54
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55 <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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56
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57 <param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level"
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58 help="Level(s) at which metrics will be accumulated">
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59 <option value="ALL_READS" selected="true">All reads (default)</option>
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60 <option value="SAMPLE" default="true">Sample</option>
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61 <option value="LIBRARY" default="true">Library</option>
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62 <option value="READ_GROUP" default="true">Read group</option>
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63 </param>
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64
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65 <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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66 </inputs>
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67 <outputs>
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68 <data format="html" name="html_file" label="${out_prefix}.html"/>
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69 </outputs>
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70 <tests>
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71 <test>
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72 <!-- python picard_wrapper.py
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73 -i "/home/~/PICARD-in.sam"
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74 -d "/home/~/outputrnaseqùetrics_files"
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75 -t "/home/~/outputrnaseqmetrics.htm"
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76 -n "RNA-Seq Metrics"
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77 --tmpdir "/home/dorine/galaxypicard/galaxy-central/database/tmp"
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78 --assumesorted true
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79 --refflat /home/~/refFlat.txt --malevel "ALL_READS" --minlength 500 --strandspecificity NONE
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80 --rrnafragmentpercentage 0.8 -j "/home/~/CollectRnaSeqMetrics.jar" -->
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81 <param name="inputFile" value="PICARD-in.sam" />
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82 <param name="out_prefix" value="RNA-Seq Metrics" />
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83 <param name="ASSUME_SORTED" value="true" />
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84 <param name="REF_FLAT" value="refFlat.txt" />
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85 <param name="malevel" value="ALL_READS" />
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86 <param name="MINIMUM_LENGTH" value="500" />
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87 <param name="STRAND_SPECIFICITY" value="NONE" />
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88 <param name="RRNA_FRAGMENT_PERCENTAGE" value="0.8" />
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89 <output name="html_file" file="outputrnaseqmetrics.html" ftype="html" lines_diff="30"/>
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90 </test>
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91 </tests>
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92 <help>
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93 Picard documentation says:
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94
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95
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96 CollectRnaSeqMetrics
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97
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98 Documentation: http://picard.sourceforge.net/command-line-overview.shtml#CollectRnaSeqMetrics
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99
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100 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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101
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102 </help>
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103 </tool>
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