comparison control_freec.xml @ 2:f923c54a17ee draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"
author iuc
date Sat, 13 Nov 2021 18:28:40 +0000
parents 2c6349fb175c
children
comparison
equal deleted inserted replaced
1:2c6349fb175c 2:f923c54a17ee
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 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="xrefs"/>
7 <requirement type="package" version="5.0.1">gawk</requirement> 7 <expand macro="requirements"/>
8 <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
11 #if str($reference_source.ref_selector) == 'history': 9 #if str($reference_source.ref_selector) == 'history':
12 ln -s '$reference_source.ref' ./genome.fa && 10 ln -s '$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 && 11 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 &&
14 #else 12 #else
28 mkdir ./output && 26 mkdir ./output &&
29 27
30 awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa && 28 awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa &&
31 29
32 ln -s '$WGS_WES.input_sample_file' ./sample.bam && 30 ln -s '$WGS_WES.input_sample_file' ./sample.bam &&
33 #if $input_control_file 31 #if $WGS_WES.input_control_file
34 ln -s '$WGS_WES.input_control_file' ./control.bam && 32 ln -s '$WGS_WES.input_control_file' ./control.bam &&
35 #end if 33 #end if
36 34
37 freec 35 freec
38 -conf '$script_file' 36 -conf '$script_file'
95 mateFile = sample.bam 93 mateFile = sample.bam
96 inputFormat = BAM 94 inputFormat = BAM
97 mateOrientation = $WGS_WES.mateOrientation_selector 95 mateOrientation = $WGS_WES.mateOrientation_selector
98 96
99 [control] 97 [control]
98 #if $WGS_WES.input_control_file
100 mateFile = control.bam 99 mateFile = control.bam
101 inputFormat = BAM 100 inputFormat = BAM
102 mateOrientation = $WGS_WES.mateOrientation_selector 101 mateOrientation = $WGS_WES.mateOrientation_selector
102 #end if
103 103
104 #if int($WGS_WES.advanced_settings.window_section.window) == 0 104 #if int($WGS_WES.advanced_settings.window_section.window) == 0
105 [target] 105 [target]
106 captureRegions = capture.bed 106 captureRegions = capture.bed
107 #end if 107 #end if
113 <option value="WGS" selected="True">whole-genome sequencing (WGS)</option> 113 <option value="WGS" selected="True">whole-genome sequencing (WGS)</option>
114 <option value="WES">whole-exome sequencing (WES)</option> 114 <option value="WES">whole-exome sequencing (WES)</option>
115 <option value="other">other method</option> 115 <option value="other">other method</option>
116 </param> 116 </param>
117 <when value="WGS"> 117 <when value="WGS">
118 <expand macro="def_input_files" /> 118 <expand macro="wgs_input_files" />
119 <section name="advanced_settings" title="Advanced WGS settings" expanded="false"> 119 <section name="advanced_settings" title="Advanced WGS settings" expanded="false">
120 <expand macro="WGS" /> 120 <expand macro="WGS" />
121 <expand macro="shared" /> 121 <expand macro="shared" />
122 </section> 122 </section>
123 </when> 123 </when>
139 <expand macro="reference_interface" /> 139 <expand macro="reference_interface" />
140 <expand macro="output_section" /> 140 <expand macro="output_section" />
141 </inputs> 141 </inputs>
142 <outputs> 142 <outputs>
143 <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" /> 143 <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" />
144 <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn" /> 144 <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn">
145 <filter>WGS_WES['input_control_file']</filter>
146 </data>
145 <data name="out_sample_coord" format="tabular" label="${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 ${on_string}: Coordinates of predicted CN alterations" from_work_dir="output/sample.bam_CNVs" />
146 <data name="out_sample_info" format="txt" label="${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 ${on_string}: Information about FREEC run" from_work_dir="output/sample.bam_info.txt" />
147 <data name="out_sample_ratio" format="tabular" label="${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 ${on_string}: Ratios and predicted CN alterations for each window" from_work_dir="output/sample.bam_ratio.txt" />
148 <data name="out_sample_subclones" format="txt" label="${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" >
149 <filter>int(WGS_WES['advanced_settings']['minimalSubclonePresence']) != 100</filter> 151 <filter>int(WGS_WES['advanced_settings']['minimalSubclonePresence']) != 100</filter>
255 <has_text text="Chromosome"/> 257 <has_text text="Chromosome"/>
256 </assert_contents> 258 </assert_contents>
257 </output> 259 </output>
258 <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" /> 260 <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" />
259 </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>
260 </tests> 279 </tests>
261 <help><![CDATA[ 280 <help><![CDATA[
262 Control-FREEC 281 Control-FREEC
263 ============= 282 =============
264 283