Mercurial > repos > mvdbeek > bam_readtagger

comparison plot_coverage.xml @ 70:94731adae3e4 draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
author mvdbeek
date Mon, 23 Mar 2020 14:23:31 +0000
parents 44f5ed2c9a26
children 156c4b5f3f38
comparison
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69:44f5ed2c9a26 70:94731adae3e4
1 <tool id="plot_coverage" name="Plot coverage" version="0.5.21"> 1 <tool id="plot_coverage" name="Plot coverage" version="0.5.22">
2 <description>as area plot between BAM files</description> 2 <description>as area plot between BAM files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5.21">readtagger</requirement> 4 <requirement type="package" version="0.5.22">readtagger</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[ 6 <command detect_errors="aggressive"><![CDATA[
7 #import re 7 #import re
8 #set identifier1 = re.sub('[^\w\-_\.\,]', '_', str( $input1.element_identifier)) 8 plot_coverage
9 #set identifier2 = re.sub('[^\w\-_\.\,]', '_', str( $input2.element_identifier)) 9 #for $r in $input_files
10 plot_coverage '$input1' '$identifier1' '$input2' '$identifier2' output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' 10 #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier))
11 --file '$r.input' '$identifier' $r.total_reads
12 #end for
13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions'
11 ]]></command> 14 ]]></command>
12 <inputs> 15 <inputs>
13 <param name="input1" type="data" format="bam,cram" label="Select a BAM file to plot"/> 16 <repeat name="input_files" title="Add input files to coverage plot" min="1">
14 <param name="input2" type="data" format="bam,cram" label="Select a second BAM file to plot" optional="true"/> 17 <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/>
18 <param name="total_reads" type="integer" value="0" min="0" label="Total number of (mapped) reads. If given plot scale will be reads per million"/>
19 </repeat>
15 <param name="regions" type="text" label="Select regions to plot" optional="true" help="e.g X:1200000-1250000,X1250000-1300000. If left blank will plot all contigs/chromosomes."> 20 <param name="regions" type="text" label="Select regions to plot" optional="true" help="e.g X:1200000-1250000,X1250000-1300000. If left blank will plot all contigs/chromosomes.">
16 <sanitizer> 21 <sanitizer>
17 <valid initial="string.letters,string.digits"> 22 <valid initial="string.letters,string.digits">
18 <add value="-" /> 23 <add value="-" />
19 <add value="," /> 24 <add value="," />
25 <outputs> 30 <outputs>
26 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> 31 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
27 </outputs> 32 </outputs>
28 <tests> 33 <tests>
29 <test> 34 <test>
30 <param name="input1" value="three_cluster_out.bam" ftype="bam"/> 35 <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
31 <param name="input2" value="three_cluster_out.bam" ftype="bam"/> 36 <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/>
37 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
38 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
32 <param name="regions" value="3R:13373525-13373615"/> 39 <param name="regions" value="3R:13373525-13373615"/>
33 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/> 40 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
34 </test> 41 </test>
35 </tests> 42 </tests>
36 <help><![CDATA[ 43 <help><![CDATA[