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comparison control_freec.xml @ 2:74cb429038c1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
author iuc
date Sat, 13 Nov 2021 18:28:07 +0000
parents 1204e79d3a99
children
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1:1204e79d3a99 2:74cb429038c1
1 <tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@"> 1 <tool id="control_freec" name="Control-FREEC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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>
6 <macros> 3 <macros>
7 <import>macros.xml</import> 4 <import>macros.xml</import>
8 </macros> 5 </macros>
9 <requirements> 6 <expand macro="xrefs"/>
10 <requirement type="package" version="5.0.1">gawk</requirement> 7 <expand macro="requirements"/>
11 <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement>
12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
14 #if str($reference_source.ref_selector) == 'history': 9 #if str($reference_source.ref_selector) == 'history':
15 ln -s '$reference_source.ref' ./genome.fa && 10 ln -s '$reference_source.ref' ./genome.fa &&
16 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 && 11 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 &&
17 #else 12 #else
31 mkdir ./output && 26 mkdir ./output &&
32 27
33 awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa && 28 awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa &&
34 29
35 ln -s '$WGS_WES.input_sample_file' ./sample.bam && 30 ln -s '$WGS_WES.input_sample_file' ./sample.bam &&
36 #if $input_control_file 31 #if $WGS_WES.input_control_file
37 ln -s '$WGS_WES.input_control_file' ./control.bam && 32 ln -s '$WGS_WES.input_control_file' ./control.bam &&
38 #end if 33 #end if
39 34
40 freec 35 freec
41 -conf '$script_file' 36 -conf '$script_file'
98 mateFile = sample.bam 93 mateFile = sample.bam
99 inputFormat = BAM 94 inputFormat = BAM
100 mateOrientation = $WGS_WES.mateOrientation_selector 95 mateOrientation = $WGS_WES.mateOrientation_selector
101 96
102 [control] 97 [control]
98 #if $WGS_WES.input_control_file
103 mateFile = control.bam 99 mateFile = control.bam
104 inputFormat = BAM 100 inputFormat = BAM
105 mateOrientation = $WGS_WES.mateOrientation_selector 101 mateOrientation = $WGS_WES.mateOrientation_selector
102 #end if
106 103
107 #if int($WGS_WES.advanced_settings.window_section.window) == 0 104 #if int($WGS_WES.advanced_settings.window_section.window) == 0
108 [target] 105 [target]
109 captureRegions = capture.bed 106 captureRegions = capture.bed
110 #end if 107 #end if
116 <option value="WGS" selected="True">whole-genome sequencing (WGS)</option> 113 <option value="WGS" selected="True">whole-genome sequencing (WGS)</option>
117 <option value="WES">whole-exome sequencing (WES)</option> 114 <option value="WES">whole-exome sequencing (WES)</option>
118 <option value="other">other method</option> 115 <option value="other">other method</option>
119 </param> 116 </param>
120 <when value="WGS"> 117 <when value="WGS">
121 <expand macro="def_input_files" /> 118 <expand macro="wgs_input_files" />
122 <section name="advanced_settings" title="Advanced WGS settings" expanded="false"> 119 <section name="advanced_settings" title="Advanced WGS settings" expanded="false">
123 <expand macro="WGS" /> 120 <expand macro="WGS" />
124 <expand macro="shared" /> 121 <expand macro="shared" />
125 </section> 122 </section>
126 </when> 123 </when>
142 <expand macro="reference_interface" /> 139 <expand macro="reference_interface" />
143 <expand macro="output_section" /> 140 <expand macro="output_section" />
144 </inputs> 141 </inputs>
145 <outputs> 142 <outputs>
146 <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" /> 143 <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" />
147 <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn" /> 144 <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn">
145 <filter>WGS_WES['input_control_file']</filter>
146 </data>
148 <data name="out_sample_coord" format="tabular" label="${tool.name} on ${on_string}: Coordinates of predicted CN alterations" from_work_dir="output/sample.bam_CNVs" /> 147 <data name="out_sample_coord" format="tabular" label="${tool.name} on ${on_string}: Coordinates of predicted CN alterations" from_work_dir="output/sample.bam_CNVs" />
149 <data name="out_sample_info" format="txt" label="${tool.name} on ${on_string}: Information about FREEC run" from_work_dir="output/sample.bam_info.txt" /> 148 <data name="out_sample_info" format="txt" label="${tool.name} on ${on_string}: Information about FREEC run" from_work_dir="output/sample.bam_info.txt" />
150 <data name="out_sample_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratios and predicted CN alterations for each window" from_work_dir="output/sample.bam_ratio.txt" /> 149 <data name="out_sample_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratios and predicted CN alterations for each window" from_work_dir="output/sample.bam_ratio.txt" />
151 <data name="out_sample_subclones" format="txt" label="${tool.name} on ${on_string}: Subclones" from_work_dir="output/sample.bam_subclones.txt" > 150 <data name="out_sample_subclones" format="txt" label="${tool.name} on ${on_string}: Subclones" from_work_dir="output/sample.bam_subclones.txt" >
152 <filter>int(WGS_WES['advanced_settings']['minimalSubclonePresence']) != 100</filter> 151 <filter>int(WGS_WES['advanced_settings']['minimalSubclonePresence']) != 100</filter>
258 <has_text text="Chromosome"/> 257 <has_text text="Chromosome"/>
259 </assert_contents> 258 </assert_contents>
260 </output> 259 </output>
261 <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" /> 260 <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" />
262 </test> 261 </test>
262 <!-- Test without control file-->
263 <test expect_num_outputs="4">
264 <conditional name="reference_source">
265 <param name="ref_selector" value="history"/>
266 <param name="ref" ftype="fasta" value="genome.fasta" />
267 </conditional>
268 <param name="WGS_WES_selector" value="WGS" />
269 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
270 <param name="mateOrientation_selector" value="0" />
271 <param name="minimalSubclonePresence" value="100" />
272 <param name="window" value="50" />
273 <param name="step" value="10" />
274 <output name="out_sample_raw" file="output/sample.bam_sample_woc.cpn" />
275 <output name="out_sample_coord" file="output/sample_woc.bam_CNVs" />
276 <output name="out_sample_info" file="output/sample.bam_info_woc.txt" />
277 <output name="out_sample_ratio" file="output/sample.bam_ratio_woc.txt" />
278 </test>
263 </tests> 279 </tests>
264 <help><![CDATA[ 280 <help><![CDATA[
265 Control-FREEC 281 Control-FREEC
266 ============= 282 =============
267 283