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comparison coverage.xml @ 0:283ab3112eea draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
author iuc
date Tue, 16 May 2023 13:14:57 +0000
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children 5602cbf1153b
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-1:000000000000 0:283ab3112eea
1 <tool id="cnvkit_coverage" name="CNVkit Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Calculate coverage in the given regions from BAM read depths</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 '$input_bam_file' ./tumor.bam &&
10 ln -s '$input_interval_bed' ./capture.split.bed &&
11 #if $reference_source.fasta
12 #if str($reference_source.ref_selector) == 'history':
13 ln -s '$reference_source.fasta' ./genome.fa &&
14 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
15 #else
16 ln -s '$reference_source.fasta.fields.path' ./genome.fa &&
17 ln -s '${reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
18 #end if
19 #end if
20 #import os
21 cnvkit.py coverage
22 ./tumor.bam
23 ./capture.split.bed
24 --output sample.targetcoverage.cnn
25 --processes \${GALAXY_SLOTS:-4}
26 $count
27 #if str($min_mapq)
28 --min-mapq $min_mapq
29 #end if
30 ]]></command>
31 <inputs>
32 <param name="input_bam_file" type="data" format="bam" label="Sample BAM file" help="" />
33 <param name="input_interval_bed" type="data" format="bed" label="Interval BED file" help="" />
34 <expand macro="reference_interface"/>
35 <param argument="--count" type="boolean" checked="false" truevalue="--count" falsevalue="" label="Get read depths by counting read midpoints within each bin" help="" />
36 <param argument="--min-mapq" optional="true" type="integer" label="Minimum mapping quality score to count a read for coverage depth" min="0" max="60" value="0" help="" />
37 </inputs>
38 <outputs>
39 <data name="out_capture_target_coverage" format="tabular" label="${tool.name} on ${on_string}: Sample Target coverage" from_work_dir="sample.targetcoverage.cnn" />
40 </outputs>
41 <tests>
42 <test expect_num_outputs="1">
43 <conditional name="reference_source">
44 <param name="ref_selector" value="history"/>
45 <param name="fasta" ftype="fasta" value="genome.fasta" />
46 </conditional>
47 <param name="input_bam_file" ftype="bam" value="tumor.bam" />
48 <param name="input_interval_bed" ftype="bed" value="capture.split.bed" />
49 <output name="out_capture_target_coverage" file="sample.targetcoverage.cnn" />
50 </test>
51 <test expect_num_outputs="1">
52 <conditional name="reference_source">
53 <param name="ref_selector" value="cached"/>
54 <param name="fasta" value="test_buildid"/>
55 </conditional>
56 <param name="input_bam_file" ftype="bam" value="tumor.bam" />
57 <param name="input_interval_bed" ftype="bed" value="capture.split.bed" />
58 <output name="out_capture_target_coverage" file="sample.targetcoverage.cnn" />
59 </test>
60 </tests>
61 <help><![CDATA[
62 Summary statistics of read counts and their binning are printed to standard error
63 when CNVkit finishes calculating the coverage of each sample (through either the
64 batch or coverage commands)
65
66 Target and antitarget bin-level coverages (.cnn) output file contains those columns
67 chromosome, Start, end, gene, log2 and depth
68 ]]></help>
69 <expand macro="citations" />
70 </tool>