Mercurial > repos > artbio > lumpy_smoove

annotate lumpy_smoove.xml @ 1:41e68da5c0fe draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
author artbio
date Tue, 25 Aug 2020 12:48:08 -0400
parents ee8fc44b1655
children 49a8a327cc72
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ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.0">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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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"
artbio
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3 <macros>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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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"
artbio
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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"
artbio
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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"
artbio
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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@
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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15 ln -s $normal_bam normal.bam &&
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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16 ln -s $tumor_bam tumor.bam &&
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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17
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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18 smoove call -x --name output
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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19 #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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20 --exclude $bedmask
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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21 #end if
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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22 --fasta reference.fa -p 24 normal.bam tumor.bam &&
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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23 gunzip output-smoove.vcf.gz
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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24 #if $prpos=="no":
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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25 && sed -i -E 's/;PRPOS=.+\tGT/\tGT/g' output-smoove.vcf
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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26 #end if
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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27
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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28
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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29 ]]></command>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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30 <inputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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31 <expand macro="reference_source_conditional" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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32 <param format="bam" name="normal_bam" type="data" label="BAM alignments from the normal sample"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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33 <param format="bam" name="tumor_bam" type="data" label="BAM alignments from the tumor sample"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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34 <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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35 <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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36 <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"
artbio
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37 <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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38 </param>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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39 <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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40 <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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41 </when>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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42 <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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43 </when>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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44 </conditional>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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45 <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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46 <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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47 <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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48 </param>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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49 </inputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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50
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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51 <outputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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52 <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.vcf" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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53 </outputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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54
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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55 <tests>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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56 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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57 <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"
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58 <param name="ref_file" value="chrI-ce11.fa"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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59 <param name="normal_bam" value="celegans_1.bam"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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60 <param name="tumor_bam" value="celegans_2.bam"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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61 <param name="choices" value="yes"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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62 <param name="bedmask" value="exclude.bed"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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63 <param name="prpos" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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64 <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="4"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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65 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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66 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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67 <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"
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68 <param name="ref_file" value="chrI-ce11.fa"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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69 <param name="normal_bam" value="celegans_1.bam"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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70 <param name="tumor_bam" value="celegans_2.bam"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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71 <param name="choices" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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72 <param name="prpos" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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73 <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="4"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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74 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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75 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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76 <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"
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77 <param name="ref_file" value="chrI-ce11.fa"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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78 <param name="normal_bam" value="celegans_2.bam"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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79 <param name="tumor_bam" value="celegans_1.bam"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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80 <param name="choices" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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81 <param name="prpos" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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82 <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="4"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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83 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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84 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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85 <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
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86 <param name="ref_file" value="chrI-ce11.fa"/>
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87 <param name="normal_bam" value="celegans_1.bam"/>
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88 <param name="tumor_bam" value="celegans_2.bam"/>
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89 <param name="choices" value="no"/>
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90 <param name="prpos" value="yes"/>
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91 <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="4"/>
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92 </test>
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93
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94 </tests>
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95
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96 <help>
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97
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98 **smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves
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99 specificity by removing many spurious alignment signals that are indicative of low-level
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artbio
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100 noise and often contribute to spurious calls.
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101
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102 There is a blog-post describing smoove in more detail
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103 here: https://brentp.github.io/post/smoove/
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104
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105 Currently, this Galaxy tool only wraps smoove for 2 samples (bam normal and tumor inputs),
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106 which translates in the command line::
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107
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108 <![CDATA[smoove call -x --name my-cohort --exclude $bed --fasta $fasta -p $threads /path/to/*.bam]]>
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109
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110 Note that the --genotype option which allows to stream smoove to svtyper is not implemented
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111 due to an error returned by svtyper in the smoove conda environment
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112
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113 the --exclude $bed is highly recommended as it can be used to ignore reads that overlap
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114 problematic regions.
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115
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116 A good set of regions for GRCh37 is https://github.com/hall-lab/speedseq/blob/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed
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117
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118 And for hg38 https://github.com/hall-lab/speedseq/blob/master/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed
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119
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120 smoove will::
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121
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122 1. parallelize calls to lumpy_filter to extract split and discordant reads required by lumpy
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123
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124 2. further filter lumpy_filter calls to remove high-coverage, spurious regions and user-specified chroms like 'hs37d5';
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125 it will also remove reads that we've found are likely spurious signals. after this, it will
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126 remove singleton reads (where the mate was removed by one of the previous filters)
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127 from the discordant bams. This makes lumpy much faster and less memory-hungry.
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128
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129 3. calculate per-sample metrics for mean, standard deviation, and distribution of insert
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130 size as required by lumpy.
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131
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132 4. stream output of lumpy directly into multiple svtyper processes for parallel-by-region
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133 genotyping while lumpy is still running. This option in not currently implemented in Galaxy
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134
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135 5. sort, compress, and index final VCF.
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136
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137 **Input(s)**
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138
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139
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140 *BAM files*: One Bam for normal sample and one Bam for tumor sample.
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141 Only BAM alignments produced by BWA-mem have been tested with this tool
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142
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143 *A bed file* describing the regions to exclude from the analysis
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144
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145
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146 *Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84)
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147
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148 .. _repository: https://github.com/brentp/smoove
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149
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150
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151 Options::
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152
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153 <![CDATA[
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154
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155 smoove calls several programs. Those with 'Y' are found on your $PATH. Only those with '*' are required.
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156
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157 [Y] bgzip [ sort -> (compress) -> index ]
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158 [Y] gsort [(sort) -> compress -> index ]
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159 [Y] tabix [ sort -> compress -> (index)]
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160 [Y] lumpy
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161 [Y] lumpy_filter
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162 [Y] samtools
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163 [Y] svtyper
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164 [Y] mosdepth [extra filtering of split and discordant files for better scaling]
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165
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166 [Y] duphold [(optional) annotate calls with depth changes]
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167 [Y] svtools [only needed for large cohorts].
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168
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169 Available sub-commands are below. Each can be run with -h for additional help.
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170
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171 call : call lumpy (and optionally svtyper)
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172 merge : merge and sort (using svtools) calls from multiple samples
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173 genotype : parallelize svtyper on an input VCF
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174 paste : square final calls from multiple samples (each with same number of variants)
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175 plot-counts : plot counts of split, discordant reads before, after smoove filtering
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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176 annotate : annotate a VCF with gene and quality of SV call
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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177 hipstr : run hipSTR in parallel
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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178 cnvnator : run cnvnator in parallel
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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179 duphold : run duphold in parallel (this can be done by adding a flag to call or genotype)
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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180 ]]>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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181 </help>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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182
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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183 <citations>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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184 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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185 </citations>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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186 </tool>