Mercurial > repos > mvdbeek > bam_readtagger

comparison plot_coverage.xml @ 78:6178c24ddd5a draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
author mvdbeek
date Tue, 07 Apr 2020 08:57:47 -0400
parents b9b76f9a816c
children c42dd2551c9c
comparison
equal deleted inserted replaced
77:b9b76f9a816c 78:6178c24ddd5a
1 <tool id="plot_coverage" name="Plot coverage" version="0.5.23"> 1 <tool id="plot_coverage" name="Plot coverage" version="0.5.24">
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="0.5.23">readtagger</requirement> 4 <requirement type="package" version="0.5.24">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 plot_coverage 8 plot_coverage
9 #for $r in $input_files 9 #for $r in $input_files
10 #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier)) 10 #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier))
11 --file '$r.input' '$identifier' $r.total_reads 11 --file '$r.input' '$identifier' $r.total_reads
12 #end for 12 #end for
13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' 13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind
14 ]]></command> 14 ]]></command>
15 <inputs> 15 <inputs>
16 <repeat name="input_files" title="Add input files to coverage plot" min="1"> 16 <repeat name="input_files" title="Add input files to coverage plot" min="1">
17 <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/> 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"/> 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"/>
25 <add value=":" /> 25 <add value=":" />
26 <add value="." /> 26 <add value="." />
27 </valid> 27 </valid>
28 </sanitizer> 28 </sanitizer>
29 </param> 29 </param>
30 <param name="plot_kind" type="select" label="Select the plot type">
31 <option value="area">Area plot</option>
32 <option value="line">Line plot</option>
33 </param>
30 </inputs> 34 </inputs>
31 <outputs> 35 <outputs>
32 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> 36 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
33 </outputs> 37 </outputs>
34 <tests> 38 <tests>
38 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/> 42 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
39 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/> 43 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
40 <param name="regions" value="3R:13373525-13373615"/> 44 <param name="regions" value="3R:13373525-13373615"/>
41 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/> 45 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
42 </test> 46 </test>
47 <test>
48 <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
49 <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/>
50 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
51 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
52 <param name="regions" value="3R:13373525-13373615"/>
53 <param name="plot_kind" value="line"/>
54 <output name="output" file="three_cluster_plot_line.pdf" ftype="pdf" compare="sim_size"/>
55 </test>
43 </tests> 56 </tests>
44 <help><![CDATA[ 57 <help><![CDATA[
45 58
46 This tool plots the coverage over a specified region (by default all chromosomes/contigs). 59 This tool plots the coverage over a specified region (by default all chromosomes/contigs).
47 60