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comparison fix.xml @ 4:bb7d5c3b4432 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 11:50:52 +0000
parents 35cc8ebecffc
children
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equal deleted inserted replaced
3:11097d7e9eed 4:bb7d5c3b4432
30 $no_gc 30 $no_gc
31 $no_edge 31 $no_edge
32 $no_rmask 32 $no_rmask
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <param name="input_target_file" type="data" format="bam" label="Sample Target coverage cnn file" help="" /> 35 <param name="input_target_file" type="data" format="cnn" label="Sample Target coverage cnn 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_antitarget_file" type="data" optional="true" format="cnn" label="Sample Antitarget coverage cnn file" 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 name="input_reference_coverage_file" type="data" optional="true" format="cnn" label="Reference coverage cnn file" help="TAS-on-target coverage cnn file is also accepted" />
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="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" />
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="--sample-id" type="text" label="Sample ID for target/antitarget files" help="Otherwise inferred from file names" />
40 <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="" />
41 <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="" />
42 <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="" />
43 </inputs> 43 </inputs>
44 <outputs> 44 <outputs>
45 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="sample.cnr" /> 45 <data name="out_sample_cnr" format="cnr" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="sample.cnr" />
46 </outputs> 46 </outputs>
47 <tests> 47 <tests>
48 <test expect_num_outputs="1"> 48 <test expect_num_outputs="1">
49 <param name="input_target_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> 49 <param name="input_target_file" ftype="cnn" value="tumor.targetcoverage.cnn" />
50 <param name="input_antitarget_file" ftype="tabular" value="tumor.antitargetcoverage.cnn" /> 50 <param name="input_antitarget_file" ftype="cnn" value="tumor.antitargetcoverage.cnn" />
51 <param name="input_reference_coverage_file" ftype="tabular" value="ref-tas.cnn" /> 51 <param name="input_reference_coverage_file" ftype="cnn" value="ref-tas.cnn" />
52 <param name="no_edge" value="1" /> 52 <param name="no_edge" value="1" />
53 <output name="out_sample_cnr"> 53 <output name="out_sample_cnr">
54 <assert_contents><has_text text="chromosome"/></assert_contents> 54 <assert_contents><has_text text="chromosome"/></assert_contents>
55 </output> 55 </output>
56 </test> 56 </test>