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comparison fix.xml @ 1:dc0fb5f07231 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:42:57 +0000
parents f64acbe71392
children
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0:f64acbe71392 1:dc0fb5f07231
2 <description>Adjust raw coverage data</description> 2 <description>Adjust raw coverage data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="creators"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_target_file' ./tumor.targetcoverage.cnn && 10 ln -s '$input_target_file' ./tumor.targetcoverage.cnn &&
10 #if $input_antitarget_file 11 #if $input_antitarget_file
11 ln -s '$input_antitarget_file' ./tumor.antitargetcoverage.cnn && 12 ln -s '$input_antitarget_file' ./tumor.antitargetcoverage.cnn &&
29 $no_gc 30 $no_gc
30 $no_edge 31 $no_edge
31 $no_rmask 32 $no_rmask
32 ]]></command> 33 ]]></command>
33 <inputs> 34 <inputs>
34 <param name="input_target_file" type="data" format="bam" label="Target coverage file" help="" /> 35 <param name="input_target_file" type="data" format="bam" label="Sample Target coverage cnn file" help="" />
35 <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Antitarget coverage file" help="" /> 36 <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Sample Antitarget coverage cnn file" help="" />
36 <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage" help="" /> 37 <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage cnn file" help="TAS-on-target coverage cnn file is also accepted" />
37 <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" /> 38 <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" />
38 <param argument="--sample-id" optional="true" type="text" label="Sample ID for target/antitarget files" value="" help="Otherwise inferred from file names" /> 39 <param argument="--sample-id" optional="true" type="text" label="Sample ID for target/antitarget files" value="" help="Otherwise inferred from file names" />
39 <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" /> 40 <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" />
40 <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="Skip edge-effect correction" help="" /> 41 <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="Skip edge-effect correction" help="" />
41 <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label=" Skip RepeatMasker correction" help="" /> 42 <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label=" Skip RepeatMasker correction" help="" />
42 </inputs> 43 </inputs>
43 <outputs> 44 <outputs>
44 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Sample copy number ratios table" from_work_dir="sample.cnr" /> 45 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="sample.cnr" />
45 </outputs> 46 </outputs>
46 <tests> 47 <tests>
47 <test expect_num_outputs="1"> 48 <test expect_num_outputs="1">
48 <param name="input_target_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> 49 <param name="input_target_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
49 <param name="input_antitarget_file" ftype="tabular" value="tumor.antitargetcoverage.cnn" /> 50 <param name="input_antitarget_file" ftype="tabular" value="tumor.antitargetcoverage.cnn" />