Mercurial > repos > artbio > lumpy_smoove

annotate lumpy_smoove.xml @ 5:bd4135caa3fa draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
author artbio
date Fri, 25 Sep 2020 10:43:20 +0000
parents 49da975ba395
children ad8853ee9909
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rev   line source
5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
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1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy5">
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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2 <description>find structural variants using the smoove workflow</description>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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3 <macros>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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4 <import>macro_lumpy_smoove.xml</import>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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5 </macros>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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6 <requirements>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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7 <requirement type="package" version="0.2.5">smoove</requirement>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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8 </requirements>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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9 <stdio>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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10 <exit_code range="1:" level="fatal" description="Tool exception" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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11 </stdio>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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12 <command detect_errors="exit_code"><![CDATA[
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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13 @pipefail@
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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14 @set_fasta_index@
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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15 #if $set_plan.plan_choice=='pair':
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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16 ln -s $set_plan.normal_bam normal.bam &&
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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17 ln -f -s $set_plan.normal_bam.metadata.bam_index normal.bam.bai &&
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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18 ln -s $set_plan.tumor_bam tumor.bam &&
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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19 ln -f -s $set_plan.tumor_bam.metadata.bam_index tumor.bam.bai &&
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bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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20 #elif $set_plan.plan_choice=='single':
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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21 ln -s $set_plan.single_bam single.bam &&
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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22 ln -f -s $set_plan.single_bam.metadata.bam_index single.bam.bai &&
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bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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23 #else:
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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24 #for $sample in $set_plan.cohort:
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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25 ln -s $sample ${sample.element_identifier}.bam &&
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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26 ln -f -s $sample.metadata.bam_index ${sample.element_identifier}.bam.bai &&
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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27 #end for
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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28 ls -la &&
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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29 #end if
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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30
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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31 smoove call --name output
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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32 #if $set_exclusion.choices=="yes":
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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33 --exclude $bedmask
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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34 #end if
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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35 --fasta reference.fa
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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36 --processes \${GALAXY_SLOTS:-4}
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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37 --genotype
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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38 #if $prpos=="no":
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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39 --removepr
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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40 #end if
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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41 *.bam &&
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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42 ls -latr &&
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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43 gunzip output-smoove.genotyped.vcf.gz
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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44
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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45 ]]></command>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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46 <inputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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47 <expand macro="reference_source_conditional" />
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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48 <conditional name="set_plan">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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49 <param name="plan_choice" type="select" label="Analyse a single Bam or a pair of Bam (eg normal/tumor)" display="radio">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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50 <option value="pair" selected="true">A pair of Bam files</option>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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51 <option value="single">A single Bam</option>
5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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52 <option value="cohort">a small cohort of Bam files (less than ~40)</option>
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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53 </param>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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54 <when value="pair">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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55 <param format="bam" name="normal_bam" type="data" label="BAM alignment from the normal sample"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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56 <param format="bam" name="tumor_bam" type="data" label="BAM alignment from the tumor sample"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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57 </when>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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58 <when value="single">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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59 <param format="bam" name="single_bam" type="data" label="BAM alignment from a single sample"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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60 </when>
5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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61 <when value="cohort">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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62 <param name="cohort" type="data_collection" format="bam" label="A collection of bam files" multiple="true"/>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
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63 </when>
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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64 </conditional>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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65
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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66
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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67 <conditional name="set_exclusion">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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68 <param name="choices" type="select" label="exclude regions with a bed file" display="radio">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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69 <option value="no" selected="true">No</option>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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70 <option value="yes">Yes</option>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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71 </param>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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72 <when value="yes">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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73 <param format="bed" name="bedmask" type="data" label="BED regions to be excluded for the analysis"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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74 </when>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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75 <when value="no">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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76 </when>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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77 </conditional>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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78 <param name="prpos" type="select" label="include the PRPOS probabilities in INFO tags" display="radio">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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79 <option value="no" selected="true">No</option>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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80 <option value="yes">Yes</option>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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81 </param>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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82 </inputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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83
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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84 <outputs>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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85 <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.genotyped.vcf" />
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
86 </outputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
87
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
88 <tests>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
89 <test>
5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
90
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
91 <conditional name="set_plan">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
92 <param name="plan_choice" value="cohort"/>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
93 <param name="cohort">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
94 <collection type="list">
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
95 <element name="1" ftype="bam" value="celegans_RG_1.bam"/>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
96 <element name="2" ftype="bam" value="celegans_RG_2.bam"/>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
97 </collection>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
98 </param>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
99 </conditional>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
100 <param name="reference_source_selector" value="history" />
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
101 <param name="ref_file" value="chrI-ce11.fa"/>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
102 <param name="choices" value="yes"/>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
103 <param name="bedmask" value="exclude.bed"/>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
104 <param name="prpos" value="no"/>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
105 <output name="vcf_call" ftype="vcf" file="result-6.vcf" lines_diff="8"/>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
106 </test>
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
107 <test>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
108 <param name="reference_source_selector" value="history" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
109 <param name="ref_file" value="chrI-ce11.fa"/>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents: 2
diff changeset
110 <param name="normal_bam" value="celegans_RG_1.bam"/>
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents: 2
diff changeset
111 <param name="tumor_bam" value="celegans_RG_2.bam"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
112 <param name="choices" value="yes"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
113 <param name="bedmask" value="exclude.bed"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
114 <param name="prpos" value="no"/>
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
115 <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="8"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
116 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
117 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
118 <param name="reference_source_selector" value="history" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
119 <param name="ref_file" value="chrI-ce11.fa"/>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents: 2
diff changeset
120 <param name="normal_bam" value="celegans_RG_1.bam"/>
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents: 2
diff changeset
121 <param name="tumor_bam" value="celegans_RG_2.bam"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
122 <param name="choices" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
123 <param name="prpos" value="no"/>
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
124 <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="8"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
125 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
126 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
127 <param name="reference_source_selector" value="history" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
128 <param name="ref_file" value="chrI-ce11.fa"/>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents: 2
diff changeset
129 <param name="normal_bam" value="celegans_RG_2.bam"/>
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents: 2
diff changeset
130 <param name="tumor_bam" value="celegans_RG_1.bam"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
131 <param name="choices" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
132 <param name="prpos" value="no"/>
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
133 <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="8"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
134 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
135 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
136 <param name="reference_source_selector" value="history" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
137 <param name="ref_file" value="chrI-ce11.fa"/>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents: 2
diff changeset
138 <param name="normal_bam" value="celegans_RG_1.bam"/>
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents: 2
diff changeset
139 <param name="tumor_bam" value="celegans_RG_2.bam"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
140 <param name="choices" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
141 <param name="prpos" value="yes"/>
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
142 <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="8"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
143 </test>
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
144 <test>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
145 <param name="reference_source_selector" value="history" />
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
146 <param name="plan_choice" value="single" />
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
147 <param name="ref_file" value="chrI-ce11.fa"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
148 <param name="single_bam" value="celegans_RG_1.bam"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
149 <param name="choices" value="no"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
150 <param name="prpos" value="no"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
151 <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="8"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
parents: 3
diff changeset
152 </test>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
153 </tests>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
154
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
155 <help>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
156 **smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
157 specificity by removing many spurious alignment signals that are indicative of low-level
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
158 noise and often contribute to spurious calls.
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
159
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
160 There is a blog-post describing smoove in more detail
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
161 here: https://brentp.github.io/post/smoove/
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
162
5
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
163 Currently, this Galaxy tool only wraps smoove for 1, 2 (bam normal and tumor inputs) or
bd4135caa3fa "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
artbio
parents: 4
diff changeset
164 a small collection of samples (&lt;40),
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
165 which translates in the command line::
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
166
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
parents: 2
diff changeset
167 <![CDATA[smoove call --name my-cohort --exclude $bed --fasta $fasta -p $threads --genotype [--removepr] /path/to/*.bam]]>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
168
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
169
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
170 the --exclude $bed is highly recommended as it can be used to ignore reads that overlap
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171 problematic regions.
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172
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173 A good set of regions for GRCh37 can be found here_
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174
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175 .. _here: https://github.com/hall-lab/speedseq/blob/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed
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176
0
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177
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178 And a good set for GRCh38 can be found there_
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179
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180 .. _there: https://github.com/hall-lab/speedseq/blob/master/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed
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181
0
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182
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183 smoove will::
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184
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185 1. parallelize calls to lumpy_filter to extract split and discordant reads required by lumpy
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186
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187 2. further filter lumpy_filter calls to remove high-coverage, spurious regions and user-specified chroms like 'hs37d5';
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188 it will also remove reads that we've found are likely spurious signals. after this, it will
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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189 remove singleton reads (where the mate was removed by one of the previous filters)
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190 from the discordant bams. This makes lumpy much faster and less memory-hungry.
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191
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192 3. calculate per-sample metrics for mean, standard deviation, and distribution of insert
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193 size as required by lumpy.
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194
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195 4. stream output of lumpy directly into multiple svtyper processes for parallel-by-region
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196 genotyping while lumpy is still running.
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197
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198 5. sort, compress, and index final VCF (but this galaxy wrapper is uncompression the gzip_vcf output)
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199
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200 **Input(s)**
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201
4
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202 * BAM files: Either a pair of Bam files (e.g. normal vs tumor sample) or a single Bam file.
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203 Only BAM alignments produced by BWA-mem have been tested with this tool
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204
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205 .. class:: warningmark
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206
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207 It is mandatory for proper run of svtyper that **BAM files contain read group information**,
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208 ie the @RG tag is present and filled in each BAM file
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209
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210
3
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211 * A bed file describing the regions to exclude from the analysis
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212 * Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84)
0
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213
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214 .. _repository: https://github.com/brentp/smoove
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215
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216
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217 Options::
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218
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219 <![CDATA[
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220
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221 smoove calls several programs. Those with 'Y' are found on your $PATH. Only those with '*' are required.
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222
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223 [Y] bgzip [ sort -> (compress) -> index ]
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224 [Y] gsort [(sort) -> compress -> index ]
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225 [Y] tabix [ sort -> compress -> (index)]
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226 [Y] lumpy
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227 [Y] lumpy_filter
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228 [Y] samtools
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229 [Y] svtyper
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230 [Y] mosdepth [extra filtering of split and discordant files for better scaling]
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231
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232 [Y] duphold [(optional) annotate calls with depth changes]
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233 [Y] svtools [only needed for large cohorts].
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234
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235 Available sub-commands are below. Each can be run with -h for additional help.
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236
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237 call : call lumpy (and optionally svtyper)
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238 merge : merge and sort (using svtools) calls from multiple samples
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239 genotype : parallelize svtyper on an input VCF
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240 paste : square final calls from multiple samples (each with same number of variants)
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241 plot-counts : plot counts of split, discordant reads before, after smoove filtering
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242 annotate : annotate a VCF with gene and quality of SV call
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243 hipstr : run hipSTR in parallel
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244 cnvnator : run cnvnator in parallel
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245 duphold : run duphold in parallel (this can be done by adding a flag to call or genotype)
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246 ]]>
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247 </help>
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248
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249 <citations>
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250 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
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251 </citations>
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252 </tool>