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comparison 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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0:5330cf818142 1:1204e79d3a99
1 <tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@"> 1 <tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@">
2 <description>detects copy-number changes and allelic imbalances</description> 2 <description>detects copy-number changes and allelic imbalances</description>
3 <xrefs>
4 <xref type="bio.tools">freec</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <import>macros.xml</import> 7 <import>macros.xml</import>
5 </macros> 8 </macros>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="5.0.1">gawk</requirement> 10 <requirement type="package" version="5.0.1">gawk</requirement>
11 #if str($reference_source.ref_selector) == 'history': 14 #if str($reference_source.ref_selector) == 'history':
12 ln -s '$reference_source.ref' ./genome.fa && 15 ln -s '$reference_source.ref' ./genome.fa &&
13 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 && 16 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 &&
14 #else 17 #else
15 ln -s '$reference_source.ref.fields.path' ./genome.fa && 18 ln -s '$reference_source.ref.fields.path' ./genome.fa &&
16 ln -s '${reference_source.ref.fields.path}.fai' ./genome.fa.fai && 19 cp '${reference_source.ref.fields.path}.fai' ./genome.fa.fai &&
17 #end if 20 #end if
18 21
19 #if int($WGS_WES.advanced_settings.window_section.window) == 0 22 #if int($WGS_WES.advanced_settings.window_section.window) == 0
20 ln -s '$WGS_WES.input_capture_file' ./capture.bed && 23 ln -s '$WGS_WES.input_capture_file' ./capture.bed &&
24
25 cat ./capture.bed | cut -f 1 | sort | uniq > ./capture.bed_tmp &&
26 cp ./genome.fa.fai ./genome.fa.fai_tmp &&
27 awk 'NR==FNR{A[$1];next}($1 in A)' ./capture.bed_tmp ./genome.fa.fai_tmp > ./genome.fa.fai &&
21 #end if 28 #end if
22 29
23 mkdir ./chromosomes && 30 mkdir ./chromosomes &&
24 mkdir ./output && 31 mkdir ./output &&
25 32
40 #if $output_section.makeGraph 47 #if $output_section.makeGraph
41 && R -f `which makeGraph.R` '$WGS_WES.advanced_settings.ploidy' 'output/sample.bam_ratio.txt' 48 && R -f `which makeGraph.R` '$WGS_WES.advanced_settings.ploidy' 'output/sample.bam_ratio.txt'
42 #end if 49 #end if
43 50
44 #if $output_section.circos_data 51 #if $output_section.circos_data
45 && python '$__tool_directory__/ratio2circos.py' 52 && python '$__tool_directory__/ratio2circos.py' '$WGS_WES.advanced_settings.ploidy'
46 -i ./output/sample.bam_ratio.BedGraph
47 -p '$WGS_WES.advanced_settings.ploidy'
48 -o sample.bam_ratio_log2_circos.txt
49 #end if 53 #end if
50 ]]></command> 54 ]]></command>
51 <configfiles> 55 <configfiles>
52 <configfile name="script_file"><![CDATA[ 56 <configfile name="script_file"><![CDATA[
53 #import os 57 #import os
157 <filter>output_section['makeGraph']</filter> 161 <filter>output_section['makeGraph']</filter>
158 </data> 162 </data>
159 <data name="out_gc_profile" format="tabular" label="${tool.name} on ${on_string}: GC-content profile" from_work_dir="output/GC_profile.targetedRegions.cnp"> 163 <data name="out_gc_profile" format="tabular" label="${tool.name} on ${on_string}: GC-content profile" from_work_dir="output/GC_profile.targetedRegions.cnp">
160 <filter>int(WGS_WES['advanced_settings']['window_section']['window']) == 0</filter> 164 <filter>int(WGS_WES['advanced_settings']['window_section']['window']) == 0</filter>
161 </data> 165 </data>
162 <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos 2D-track data" from_work_dir="output/sample.bam_ratio_log2_circos.txt"> 166 <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Log2 Ratio (2D Data Track)" from_work_dir="output/sample.bam_ratio_log2_circos.txt">
167 <filter>output_section['circos_data']</filter>
168 </data>
169 <data name="out_chr_sorted_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Karyotype" from_work_dir="output/karyotype_circos.txt">
163 <filter>output_section['circos_data']</filter> 170 <filter>output_section['circos_data']</filter>
164 </data> 171 </data>
165 </outputs> 172 </outputs>
166 <tests> 173 <tests>
167 <test expect_num_outputs="5"> 174 <test expect_num_outputs="5">