annotate coverage.xml @ 1:5602cbf1153b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:41:04 +0000
parents 283ab3112eea
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283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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1 <tool id="cnvkit_coverage" name="CNVkit Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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2 <description>Calculate coverage in the given regions from BAM read depths</description>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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3 <macros>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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4 <import>macros.xml</import>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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5 </macros>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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6 <expand macro="xrefs"/>
1
5602cbf1153b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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7 <expand macro="creators"/>
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283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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8 <expand macro="requirements"/>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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9 <command detect_errors="exit_code"><![CDATA[
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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10 ln -s '$input_bam_file' ./tumor.bam &&
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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11 ln -s '$input_interval_bed' ./capture.split.bed &&
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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12 #if $reference_source.fasta
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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13 #if str($reference_source.ref_selector) == 'history':
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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14 ln -s '$reference_source.fasta' ./genome.fa &&
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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15 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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16 #else
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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17 ln -s '$reference_source.fasta.fields.path' ./genome.fa &&
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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18 ln -s '${reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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19 #end if
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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20 #end if
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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21 #import os
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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22 cnvkit.py coverage
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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23 ./tumor.bam
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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24 ./capture.split.bed
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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25 --output sample.targetcoverage.cnn
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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26 --processes \${GALAXY_SLOTS:-4}
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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27 $count
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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28 #if str($min_mapq)
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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29 --min-mapq $min_mapq
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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30 #end if
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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31 ]]></command>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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32 <inputs>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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33 <param name="input_bam_file" type="data" format="bam" label="Sample BAM file" help="" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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34 <param name="input_interval_bed" type="data" format="bed" label="Interval BED file" help="" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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35 <expand macro="reference_interface"/>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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36 <param argument="--count" type="boolean" checked="false" truevalue="--count" falsevalue="" label="Get read depths by counting read midpoints within each bin" help="" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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37 <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="" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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38 </inputs>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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39 <outputs>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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40 <data name="out_capture_target_coverage" format="tabular" label="${tool.name} on ${on_string}: Sample Target coverage" from_work_dir="sample.targetcoverage.cnn" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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41 </outputs>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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42 <tests>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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43 <test expect_num_outputs="1">
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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44 <conditional name="reference_source">
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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45 <param name="ref_selector" value="history"/>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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46 <param name="fasta" ftype="fasta" value="genome.fasta" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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47 </conditional>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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48 <param name="input_bam_file" ftype="bam" value="tumor.bam" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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49 <param name="input_interval_bed" ftype="bed" value="capture.split.bed" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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50 <output name="out_capture_target_coverage" file="sample.targetcoverage.cnn" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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51 </test>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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52 <test expect_num_outputs="1">
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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53 <conditional name="reference_source">
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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54 <param name="ref_selector" value="cached"/>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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55 <param name="fasta" value="test_buildid"/>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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56 </conditional>
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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57 <param name="input_bam_file" ftype="bam" value="tumor.bam" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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58 <param name="input_interval_bed" ftype="bed" value="capture.split.bed" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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59 <output name="out_capture_target_coverage" file="sample.targetcoverage.cnn" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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60 </test>
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61 </tests>
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62 <help><![CDATA[
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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63 Summary statistics of read counts and their binning are printed to standard error
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64 when CNVkit finishes calculating the coverage of each sample (through either the
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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65 batch or coverage commands)
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66
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67 Target and antitarget bin-level coverages (.cnn) output file contains those columns
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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68 chromosome, Start, end, gene, log2 and depth
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69 ]]></help>
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70 <expand macro="citations" />
283ab3112eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a
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71 </tool>