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comparison fix.xml @ 0:fb748ff4c83e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
author iuc
date Sun, 14 May 2023 20:06:52 +0000
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children 35cc8ebecffc
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-1:000000000000 0:fb748ff4c83e
1 <tool id="cnvkit_fix" name="CNVkit Fix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Adjust raw coverage data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_target_file' ./tumor.targetcoverage.cnn &&
10 #if $input_antitarget_file
11 ln -s '$input_antitarget_file' ./tumor.antitargetcoverage.cnn &&
12 #end if
13 #if $input_reference_coverage_file
14 ln -s '$input_reference_coverage_file' ./ref-tas.cnn &&
15 #end if
16 cnvkit.py fix
17 ./tumor.targetcoverage.cnn
18 #if $input_antitarget_file
19 ./tumor.antitargetcoverage.cnn
20 #end if
21 #if $input_reference_coverage_file
22 ./ref-tas.cnn
23 #end if
24 --output sample.cnr
25 $cluster
26 #if $sample_id
27 --sample-id '$sample_id'
28 #end if
29 $no_gc
30 $no_edge
31 $no_rmask
32 ]]></command>
33 <inputs>
34 <param name="input_target_file" type="data" format="bam" label="Target coverage file" help="" />
35 <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Antitarget coverage file" help="" />
36 <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage" help="" />
37 <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" />
38 <param argument="--sample-id" optional="true" type="text" label="Sample ID for target/antitarget files" value="" help="Otherwise inferred from file names" />
39 <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" />
40 <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="Skip edge-effect correction" help="" />
41 <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label=" Skip RepeatMasker correction" help="" />
42 </inputs>
43 <outputs>
44 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Sample copy number ratios table" from_work_dir="sample.cnr" />
45 </outputs>
46 <tests>
47 <test expect_num_outputs="1">
48 <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_reference_coverage_file" ftype="tabular" value="ref-tas.cnn" />
51 <param name="no_edge" value="1" />
52 <output name="out_sample_cnr">
53 <assert_contents><has_text text="chromosome"/></assert_contents>
54 </output>
55 </test>
56 </tests>
57 <help><![CDATA[
58 Combine the uncorrected target and antitarget coverage tables (.cnn) and correct for biases
59 in regional coverage and GC content, according to the given reference.
60
61 The reference .cnn file output contains those columns
62 chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
63 of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
64 depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
65 ]]></help>
66 <expand macro="citations" />
67 </tool>