annotate lumpyexpress.xml @ 5:9697ce23db99 draft

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author hepcat72
date Fri, 26 Oct 2018 09:30:28 -0400
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1 <tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.3">
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2 <description>Single or paired end SV detection</description>
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4 <requirements>
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5 <requirement type="package" version="2.7">python</requirement>
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6 <requirement type="package" version="0.8.3">pysam</requirement>
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7 <requirement type="package" version="1.13.1">numpy</requirement>
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8 <requirement type="package" version="0.2.13">lumpy-sv</requirement>
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9 <requirement type="package" version="1.9">samtools</requirement>
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10 <requirement type="package" version="0.1.24">samblaster</requirement>
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11 <requirement type="package" version="0.6.5">sambamba</requirement>
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12 <requirement type="package" version="4.2.1">gawk</requirement>
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13 </requirements>
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14
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15 <version_command><![CDATA[
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16 lumpy 2>&1 >/dev/null | grep Program | cut -d ' ' -f 4 | cut -d ')' -f 1
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17 ]]></version_command>
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19 <command detect_errors="aggressive">
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20 <![CDATA[
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21 $__tool_directory__/lumpy_wrapper.tcsh
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22 '$paired'
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23 '$outfile'
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24 #for $bam in $bams
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25 '$bam'
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26 #end for
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27 ]]>
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28 </command>
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30 <inputs>
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31 <param format="bam"
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32 name="bams"
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33 label="Bam file(s)"
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34 argument="argument positions 3-N"
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35
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36 type="data"
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37 multiple="true"
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39 help="Optionally sorted/indexed whole bam files. Splitters and discordants will be extracted from this file."/>
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41 <param name="paired"
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42 label="Bam files contain paired end data"
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43 argument="argument position 1"
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45 type="boolean"
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46 truevalue="1"
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47 falsevalue="0"
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48 checked="no"
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49 value="false"/>
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50 </inputs>
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52 <outputs>
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53 <data format="vcf" name="outfile" />
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54 </outputs>
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56 <tests>
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57 <test>
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58 <param name="bams" value="test1-1.bam,test1-2.bam,test1-3.bam"/>
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59 <param name="paired" value="1"/>
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60 <output name="outfile" file="lumpy-test1.vcf"/>
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61 </test>
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62 </tests>
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64 <help>
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65 <![CDATA[
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66 Paired-end data is processed with lumpyexpress using only the required arguments. Single-end data is processed with lumpy using `-mw 4 -tt 0 -sr id:<SAMPLE>,bam_file:<SAMPLE>.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20`. Submit an issue to the tool wrapper repo if you would like more options to be available: https://github.com/hepcat72/robs_galaxy_tools
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68 Split reads and discordant reads are extracted from the supplied bam files. Each bam file should represent a different sample.
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70 This is a wrapper for lumpyexpress that comes with lumpy-sv version 0.2.13. The script in the latest version of lumpy-sv (0.2.14a) has some issues when run on galaxy.
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71 ]]>
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72 </help>
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74 <citations>
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75 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
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76 </citations>
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78 </tool>