Mercurial > repos > artbio > lumpy_smoove

annotate lumpy_smoove.xml @ 4:49da975ba395 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
author artbio
date Thu, 27 Aug 2020 17:14:25 -0400
parents 65b400409455
children bd4135caa3fa
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4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.6.0">
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 &&
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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20 #else
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 &&
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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23 #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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24
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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25 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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26 #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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27 --exclude $bedmask
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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28 #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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29 --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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30 --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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31 --genotype
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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32 #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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33 --removepr
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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34 #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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35 *.bam &&
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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36 ls -latr &&
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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37 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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38
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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39 ]]></command>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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40 <inputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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41 <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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42 <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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43 <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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44 <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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45 <option value="single">A single Bam</option>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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46 </param>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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47 <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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48 <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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49 <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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50 </when>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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51 <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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52 <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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53 </when>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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54 </conditional>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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55
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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56
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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57 <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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58 <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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59 <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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60 <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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61 </param>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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62 <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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63 <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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64 </when>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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65 <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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66 </when>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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67 </conditional>
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="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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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 </inputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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73
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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74 <outputs>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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75 <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"
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76 </outputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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77
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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78 <tests>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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79 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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80 <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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81 <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"
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82 <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"
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83 <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"
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84 <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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85 <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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86 <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
87 <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
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diff changeset
88 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
89 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
90 <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
91 <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
92 <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
93 <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
94 <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
95 <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
96 <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
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97 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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98 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff changeset
99 <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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diff changeset
100 <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
101 <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
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102 <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
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diff changeset
103 <param name="choices" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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diff changeset
104 <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
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105 <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
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106 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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107 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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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
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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
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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
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112 <param name="choices" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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113 <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
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114 <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
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115 </test>
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
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116 <test>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
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117 <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
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118 <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
119 <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
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120 <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
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121 <param name="choices" value="no"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
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122 <param name="prpos" value="no"/>
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
artbio
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123 <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
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124 </test>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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125 </tests>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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126
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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127 <help>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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128 **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
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129 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
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diff changeset
130 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"
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131
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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diff changeset
132 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
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133 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"
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134
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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135 Currently, this Galaxy tool only wraps smoove for 2 samples (bam normal and tumor inputs),
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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diff changeset
136 which translates in the command line::
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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137
3
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artbio
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138 <![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"
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139
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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140
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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141 the --exclude $bed is highly recommended as it can be used to ignore reads that overlap
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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diff changeset
142 problematic regions.
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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143
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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144 A good set of regions for GRCh37 can be found here_
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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145
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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146 .. _here: https://github.com/hall-lab/speedseq/blob/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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147
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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148
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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diff changeset
149 And a good set for GRCh38 can be found there_
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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150
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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151 .. _there: https://github.com/hall-lab/speedseq/blob/master/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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152
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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153
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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154 smoove will::
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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155
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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diff changeset
156 1. parallelize calls to lumpy_filter to extract split and discordant reads required by lumpy
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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157
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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diff changeset
158 2. further filter lumpy_filter calls to remove high-coverage, spurious regions and user-specified chroms like 'hs37d5';
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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159 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"
artbio
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160 remove singleton reads (where the mate was removed by one of the previous filters)
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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diff changeset
161 from the discordant bams. This makes lumpy much faster and less memory-hungry.
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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162
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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diff changeset
163 3. calculate per-sample metrics for mean, standard deviation, and distribution of insert
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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diff changeset
164 size as required by lumpy.
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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165
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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166 4. stream output of lumpy directly into multiple svtyper processes for parallel-by-region
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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167 genotyping while lumpy is still running.
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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168
3
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artbio
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169 5. sort, compress, and index final VCF (but this galaxy wrapper is uncompression the gzip_vcf output)
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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170
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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171 **Input(s)**
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172
4
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artbio
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173 * BAM files: Either a pair of Bam files (e.g. normal vs tumor sample) or a single Bam file.
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174 Only BAM alignments produced by BWA-mem have been tested with this tool
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175
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176 .. class:: warningmark
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177
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178 It is mandatory for proper run of svtyper that **BAM files contain read group information**,
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179 ie the @RG tag is present and filled in each BAM file
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180
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181
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182 * A bed file describing the regions to exclude from the analysis
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183 * Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84)
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184
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185 .. _repository: https://github.com/brentp/smoove
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186
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187
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188 Options::
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189
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190 <![CDATA[
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191
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192 smoove calls several programs. Those with 'Y' are found on your $PATH. Only those with '*' are required.
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193
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194 [Y] bgzip [ sort -> (compress) -> index ]
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195 [Y] gsort [(sort) -> compress -> index ]
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196 [Y] tabix [ sort -> compress -> (index)]
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197 [Y] lumpy
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198 [Y] lumpy_filter
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199 [Y] samtools
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200 [Y] svtyper
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201 [Y] mosdepth [extra filtering of split and discordant files for better scaling]
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202
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203 [Y] duphold [(optional) annotate calls with depth changes]
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204 [Y] svtools [only needed for large cohorts].
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205
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206 Available sub-commands are below. Each can be run with -h for additional help.
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207
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208 call : call lumpy (and optionally svtyper)
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209 merge : merge and sort (using svtools) calls from multiple samples
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210 genotype : parallelize svtyper on an input VCF
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211 paste : square final calls from multiple samples (each with same number of variants)
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212 plot-counts : plot counts of split, discordant reads before, after smoove filtering
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213 annotate : annotate a VCF with gene and quality of SV call
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214 hipstr : run hipSTR in parallel
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215 cnvnator : run cnvnator in parallel
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216 duphold : run duphold in parallel (this can be done by adding a flag to call or genotype)
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217 ]]>
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218 </help>
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219
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220 <citations>
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221 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
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222 </citations>
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223 </tool>