Mercurial > repos > mvdbeek > bam_readtagger

comparison plot_coverage.xml @ 79:c42dd2551c9c draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a"
author mvdbeek
date Tue, 07 Apr 2020 13:41:14 -0400
parents 6178c24ddd5a
children c9361b7a025d
comparison
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78:6178c24ddd5a 79:c42dd2551c9c
1 <tool id="plot_coverage" name="Plot coverage" version="0.5.24"> 1 <tool id="plot_coverage" name="Plot coverage" version="0.5.25">
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="0.5.24">readtagger</requirement> 4 <requirement type="package" version="0.5.25">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' --plot_kind $plot_kind 13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind --style $style
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"/>
29 </param> 29 </param>
30 <param name="plot_kind" type="select" label="Select the plot type"> 30 <param name="plot_kind" type="select" label="Select the plot type">
31 <option value="area">Area plot</option> 31 <option value="area">Area plot</option>
32 <option value="line">Line plot</option> 32 <option value="line">Line plot</option>
33 </param> 33 </param>
34 <param name="style" type="select" label="Select a plotting style">
35 <option value="ggplot">ggplot</option>
36 <option value="classic">classic</option>
37 <option value="greyscale">greyscale</option>
38 <option value="dark_background">dark_background</option>
39 <option value="seaborn">seaborn</option>
40 <option value="seaborn-bright">seaborn-bright</option>
41 <option value="seaborn-colorblind">seaborn-colorblind</option>
42 <option value="seaborn-dark">seaborn-dark</option>
43 <option value="seaborn-dark-palette">seaborn-dark-palette</option>
44 <option value="seaborn-darkgrid">seaborn-darkgrid</option>
45 <option value="seaborn-deep">seaborn-deep</option>
46 <option value="seaborn-muted">seaborn-muted</option>
47 <option value="seaborn-notebook">seaborn-notebook</option>
48 <option value="seaborn-paper">seaborn-paper</option>
49 <option value="seaborn-pastel">seaborn-pastel</option>
50 <option value="seaborn-poster">seaborn-poster</option>
51 <option value="seaborn-talk">seaborn-talk</option>
52 <option value="seaborn-ticks">seaborn-ticks</option>
53 <option value="seaborn-white">seaborn-white</option>
54 <option value="seaborn-whitegrid">seaborn-whitegrid</option>
55 <option value="tableau-colorblind10">tableau-colorblind10</option>
56 </param>
34 </inputs> 57 </inputs>
35 <outputs> 58 <outputs>
36 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> 59 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
37 </outputs> 60 </outputs>
38 <tests> 61 <tests>