Mercurial > repos > iuc > control_freec

annotate control_freec.xml @ 1:1204e79d3a99 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:10:37 +0000
parents 5330cf818142
children 74cb429038c1
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5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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1 <tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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2 <description>detects copy-number changes and allelic imbalances</description>
1
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <xrefs>
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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4 <xref type="bio.tools">freec</xref>
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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5 </xrefs>
0
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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6 <macros>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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7 <import>macros.xml</import>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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8 </macros>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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9 <requirements>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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10 <requirement type="package" version="5.0.1">gawk</requirement>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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11 <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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12 </requirements>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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13 <command detect_errors="exit_code"><![CDATA[
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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14 #if str($reference_source.ref_selector) == 'history':
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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15 ln -s '$reference_source.ref' ./genome.fa &&
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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16 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 &&
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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17 #else
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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18 ln -s '$reference_source.ref.fields.path' ./genome.fa &&
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1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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19 cp '${reference_source.ref.fields.path}.fai' ./genome.fa.fai &&
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5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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20 #end if
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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21
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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22 #if int($WGS_WES.advanced_settings.window_section.window) == 0
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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23 ln -s '$WGS_WES.input_capture_file' ./capture.bed &&
1
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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24
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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25 cat ./capture.bed | cut -f 1 | sort | uniq > ./capture.bed_tmp &&
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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26 cp ./genome.fa.fai ./genome.fa.fai_tmp &&
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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27 awk 'NR==FNR{A[$1];next}($1 in A)' ./capture.bed_tmp ./genome.fa.fai_tmp > ./genome.fa.fai &&
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5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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28 #end if
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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29
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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30 mkdir ./chromosomes &&
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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31 mkdir ./output &&
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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32
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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33 awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa &&
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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34
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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35 ln -s '$WGS_WES.input_sample_file' ./sample.bam &&
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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36 #if $input_control_file
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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37 ln -s '$WGS_WES.input_control_file' ./control.bam &&
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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38 #end if
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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39
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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40 freec
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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41 -conf '$script_file'
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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42 -sample ./sample.bam
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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43 #if $WGS_WES.input_control_file
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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44 -control ./control.bam
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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45 #end if
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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46
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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47 #if $output_section.makeGraph
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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48 && R -f `which makeGraph.R` '$WGS_WES.advanced_settings.ploidy' 'output/sample.bam_ratio.txt'
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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49 #end if
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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50
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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51 #if $output_section.circos_data
1
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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52 && python '$__tool_directory__/ratio2circos.py' '$WGS_WES.advanced_settings.ploidy'
0
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53 #end if
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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54 ]]></command>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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55 <configfiles>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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56 <configfile name="script_file"><![CDATA[
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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57 #import os
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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58 #set galaxy_slots = os.getenv("GALAXY_SLOTS", 4)
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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59 [general]
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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60 chrFiles = chromosomes
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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61 outputDir = output
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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62 chrLenFile = genome.fa.fai
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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63 maxThreads = $galaxy_slots
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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64
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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65 #if $WGS_WES.advanced_settings.degree == "34"
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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66 #set $degree_val = "3&4"
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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67 degree = $degree_val
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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68 #else
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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69 degree = $WGS_WES.advanced_settings.degree
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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70 #end if
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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71 forceGCcontentNormalization = $WGS_WES.advanced_settings.forceGCcontentNormalization
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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72 minCNAlength = $WGS_WES.advanced_settings.minCNAlength
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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73 minimalSubclonePresence = $WGS_WES.advanced_settings.minimalSubclonePresence
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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74 readCountThreshold = $WGS_WES.advanced_settings.readCountThreshold
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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75 window = $WGS_WES.advanced_settings.window_section.window
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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76 step = $WGS_WES.advanced_settings.window_section.step
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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77 coefficientOfVariation = $WGS_WES.advanced_settings.coefficientOfVariation
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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78 #if $output_section.circos_data
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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79 BedGraphOutput = TRUE
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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80 #else
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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81 BedGraphOutput = $output_section.BedGraphOutput
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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82 #end if
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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83 breakPointThreshold = $WGS_WES.advanced_settings.breakPointThreshold
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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84 breakPointType = $WGS_WES.advanced_settings.breakPointType
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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85 contaminationAdjustment = $WGS_WES.advanced_settings.contaminationAdjustment
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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86 contamination = $WGS_WES.advanced_settings.contamination
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
87 intercept = $WGS_WES.advanced_settings.intercept
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
88 minMappabilityPerWindow = $WGS_WES.advanced_settings.minMappabilityPerWindow
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
89 minExpectedGC = $WGS_WES.advanced_settings.minExpectedGC
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
90 maxExpectedGC = $WGS_WES.advanced_settings.maxExpectedGC
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
91 noisyData = $WGS_WES.advanced_settings.noisyData
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
92 ploidy = $WGS_WES.advanced_settings.ploidy
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
93 printNA = $WGS_WES.advanced_settings.printNA
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
94 sex = $WGS_WES.advanced_settings.sex
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
95 telocentromeric = $WGS_WES.advanced_settings.telocentromeric
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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96
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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97 [sample]
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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98 mateFile = sample.bam
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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99 inputFormat = BAM
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
100 mateOrientation = $WGS_WES.mateOrientation_selector
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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101
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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102 [control]
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
103 mateFile = control.bam
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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104 inputFormat = BAM
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
105 mateOrientation = $WGS_WES.mateOrientation_selector
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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106
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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107 #if int($WGS_WES.advanced_settings.window_section.window) == 0
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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108 [target]
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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109 captureRegions = capture.bed
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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110 #end if
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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111 ]]></configfile>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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112 </configfiles>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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113 <inputs>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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114 <conditional name="WGS_WES">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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115 <param name="WGS_WES_selector" type="select" label="Select the sequencing method of the input file(s)" help="">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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116 <option value="WGS" selected="True">whole-genome sequencing (WGS)</option>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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117 <option value="WES">whole-exome sequencing (WES)</option>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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118 <option value="other">other method</option>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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119 </param>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
120 <when value="WGS">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
121 <expand macro="def_input_files" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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122 <section name="advanced_settings" title="Advanced WGS settings" expanded="false">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
123 <expand macro="WGS" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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124 <expand macro="shared" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
125 </section>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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126 </when>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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127 <when value="WES">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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128 <expand macro="wes_input_files" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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129 <section name="advanced_settings" title="Advanced WES settings" expanded="false">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
130 <expand macro="WES" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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131 <expand macro="shared" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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132 </section>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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133 </when>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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134 <when value="other">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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135 <expand macro="wes_input_files" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
136 <section name="advanced_settings" title="Advanced settings" expanded="true">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
137 <expand macro="other" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
138 <expand macro="shared" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
139 </section>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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140 </when>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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141 </conditional>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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142 <expand macro="reference_interface" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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143 <expand macro="output_section" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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144 </inputs>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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145 <outputs>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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146 <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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147 <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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148 <data name="out_sample_coord" format="tabular" label="${tool.name} on ${on_string}: Coordinates of predicted CN alterations" from_work_dir="output/sample.bam_CNVs" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
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149 <data name="out_sample_info" format="txt" label="${tool.name} on ${on_string}: Information about FREEC run" from_work_dir="output/sample.bam_info.txt" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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150 <data name="out_sample_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratios and predicted CN alterations for each window" from_work_dir="output/sample.bam_ratio.txt" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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151 <data name="out_sample_subclones" format="txt" label="${tool.name} on ${on_string}: Subclones" from_work_dir="output/sample.bam_subclones.txt" >
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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152 <filter>int(WGS_WES['advanced_settings']['minimalSubclonePresence']) != 100</filter>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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153 </data>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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154 <data name="out_sample_bedgraph" format="bed" label="${tool.name} on ${on_string}: Ratios in BedGraph format" from_work_dir="output/sample.bam_ratio.BedGraph">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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155 <filter>output_section['BedGraphOutput']</filter>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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156 </data>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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157 <data name="out_mg_png" format="png" label="${tool.name} on ${on_string}: Normalized CN profile" from_work_dir="output/sample.bam_ratio.txt.png">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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158 <filter>output_section['makeGraph']</filter>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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159 </data>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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160 <data name="out_mg_log2_png" format="png" label="${tool.name} on ${on_string}: Normalized CN profile (log2)" from_work_dir="output/sample.bam_ratio.txt.log2.png">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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161 <filter>output_section['makeGraph']</filter>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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162 </data>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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163 <data name="out_gc_profile" format="tabular" label="${tool.name} on ${on_string}: GC-content profile" from_work_dir="output/GC_profile.targetedRegions.cnp">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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164 <filter>int(WGS_WES['advanced_settings']['window_section']['window']) == 0</filter>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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parents:
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165 </data>
1
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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parents: 0
diff changeset
166 <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Log2 Ratio (2D Data Track)" from_work_dir="output/sample.bam_ratio_log2_circos.txt">
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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167 <filter>output_section['circos_data']</filter>
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 0
diff changeset
168 </data>
1204e79d3a99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
169 <data name="out_chr_sorted_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Karyotype" from_work_dir="output/karyotype_circos.txt">
0
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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170 <filter>output_section['circos_data']</filter>
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parents:
diff changeset
171 </data>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
172 </outputs>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
173 <tests>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
174 <test expect_num_outputs="5">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
175 <conditional name="reference_source">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
176 <param name="ref_selector" value="history"/>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
177 <param name="ref" ftype="fasta" value="genome.fasta" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
178 </conditional>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
179 <param name="WGS_WES_selector" value="other" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
180 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
181 <param name="input_control_file" ftype="bam" value="normal.bam" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
182 <param name="mateOrientation_selector" value="0" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
183 <param name="window" value="5000" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
184 <param name="step" value="1000" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
185 <output name="out_sample_raw" file="output/sample.bam_sample.cpn" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
186 <output name="out_control_raw" file="output/control.bam_control.cpn" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
187 <output name="out_sample_coord" file="output/sample.bam_CNVs" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
188 <output name="out_sample_info" file="output/sample.bam_info.txt" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
189 <output name="out_sample_ratio" file="output/sample.bam_ratio.txt" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
190 </test>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
191 <test expect_num_outputs="5">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
192 <conditional name="reference_source">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
193 <param name="ref_selector" value="cached"/>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
194 <param name="ref" value="test_buildid"/>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
195 </conditional>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
196 <param name="WGS_WES_selector" value="other" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
197 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
198 <param name="input_control_file" ftype="bam" value="normal.bam" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
199 <param name="mateOrientation_selector" value="0" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
200 <param name="window" value="5000" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
201 <param name="step" value="1000" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
202 <output name="out_sample_raw" file="output/sample.bam_sample.cpn" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
203 <output name="out_control_raw" file="output/control.bam_control.cpn" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
204 <output name="out_sample_coord" file="output/sample.bam_CNVs" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
205 <output name="out_sample_info" file="output/sample.bam_info.txt" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
206 <output name="out_sample_ratio" file="output/sample.bam_ratio.txt" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
207 </test>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
208 <test expect_num_outputs="5">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
209 <conditional name="reference_source">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
210 <param name="ref_selector" value="history"/>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
211 <param name="ref" ftype="fasta" value="genome.fasta" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
212 </conditional>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
213 <param name="WGS_WES_selector" value="WGS" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
214 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
215 <param name="input_control_file" ftype="bam" value="normal.bam" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
216 <param name="mateOrientation_selector" value="0" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
217 <param name="minimalSubclonePresence" value="100" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
218 <param name="window" value="5000" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
219 <param name="step" value="1000" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
220 <output name="out_sample_raw" file="output/sample.bam_sample.cpn" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
221 <output name="out_control_raw" file="output/control.bam_control.cpn" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
222 <output name="out_sample_coord" file="output/sample.bam_CNVs" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
223 <output name="out_sample_info" file="output/sample.bam_info.txt" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
224 <output name="out_sample_ratio" file="output/sample.bam_ratio.txt" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
225 </test>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
226 <test expect_num_outputs="6">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
227 <conditional name="reference_source">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
228 <param name="ref_selector" value="history"/>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
229 <param name="ref" ftype="fasta" value="genome.fasta" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
230 </conditional>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
231 <param name="WGS_WES_selector" value="WES" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
232 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
233 <param name="input_control_file" ftype="bam" value="normal.bam" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
234 <param name="input_capture_file" ftype="bed" value="capture.bed" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
235 <param name="mateOrientation_selector" value="0" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
236 <param name="minimalSubclonePresence" value="100" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
237 <param name="forceGCcontentNormalization" value="2" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
238 <param name="window" value="0" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
239 <param name="step" value="0" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
240 <output name="out_sample_raw">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
241 <assert_contents>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
242 <has_text_matching expression="M\t\d+\t\d+\t\d+\tM:\d+-\d+"/>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
243 </assert_contents>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
244 </output>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
245 <output name="out_control_raw">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
246 <assert_contents>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
247 <has_text_matching expression="M\t\d+\t\d+\t\d+\tM:\d+-\d+"/>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
248 </assert_contents>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
249 </output>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
250 <output name="out_sample_coord" file="output/sample.bam_CNVs" />
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
251 <output name="out_sample_info">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
252 <assert_contents>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
253 <has_text text="Program_Version"/>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
254 </assert_contents>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
255 </output>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
256 <output name="out_sample_ratio">
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff changeset
257 <assert_contents>
5330cf818142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
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258 <has_text text="Chromosome"/>
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259 </assert_contents>
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260 </output>
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261 <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" />
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262 </test>
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263 </tests>
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264 <help><![CDATA[
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265 Control-FREEC
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266 =============
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267
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268 Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including loss of heterozygosity/LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). Nowdays, Control-FREEC is supported by the team of Valentina Boeva at Institut Cochin, Inserm (Paris).
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269
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270 Control-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. The control (matched normal) sample is optional for whole genome sequencing data but mandatory for whole exome or targeted sequencing data. For whole genome sequencing data analysis, the program can also use mappability data (files created by GEM).
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271
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272 **Input for CNA detection:** Aligned single-end, paired-end or mate-pair data in BAM format.
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273
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274 **Output:** Regions of gain, loss and LOH and normalized copy number.
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275
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276 For more information (f.e. to run Control-FREEC on non-human data) see the Control-FREEC documentation_.
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277
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278 .. _documentation: http://boevalab.inf.ethz.ch/FREEC/index.html#documentation
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279
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280 ]]></help>
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281 <citations>
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282 <citation type="doi">10.1093/bioinformatics/btr670</citation>
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283 <citation type="doi">10.1093/bioinformatics/btq635</citation>
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284 </citations>
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285 </tool>