Mercurial > repos > mvdbeek > bam_readtagger

annotate plot_coverage.xml @ 78:6178c24ddd5a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
78
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
1 <tool id="plot_coverage" name="Plot coverage" version="0.5.24">
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
2 <description>as area plot between BAM files</description>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
3 <requirements>
78
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
4 <requirement type="package" version="0.5.24">readtagger</requirement>
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
5 </requirements>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
6 <command detect_errors="aggressive"><![CDATA[
75
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
7 #import re
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
8 plot_coverage
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
9 #for $r in $input_files
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
10 #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier))
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
11 --file '$r.input' '$identifier' $r.total_reads
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
12 #end for
78
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
14 ]]></command>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
15 <inputs>
75
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
16 <repeat name="input_files" title="Add input files to coverage plot" min="1">
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
17 <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/>
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
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"/>
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
19 </repeat>
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
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.">
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
21 <sanitizer>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
22 <valid initial="string.letters,string.digits">
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
23 <add value="-" />
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
24 <add value="," />
38
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
parents: 37
diff changeset
25 <add value=":" />
77
b9b76f9a816c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit dcf9c3bb0ed1b0a3011f659bd702bb47578178e7"
mvdbeek
parents: 76
diff changeset
26 <add value="." />
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
27 </valid>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
28 </sanitizer>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
29 </param>
78
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
30 <param name="plot_kind" type="select" label="Select the plot type">
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
31 <option value="area">Area plot</option>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
32 <option value="line">Line plot</option>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
33 </param>
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
34 </inputs>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
35 <outputs>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
36 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
37 </outputs>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
38 <tests>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
39 <test>
75
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
40 <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
41 <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/>
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
42 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 74
diff changeset
43 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
44 <param name="regions" value="3R:13373525-13373615"/>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
45 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
46 </test>
78
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
47 <test>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
48 <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
49 <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
50 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
51 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
52 <param name="regions" value="3R:13373525-13373615"/>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
53 <param name="plot_kind" value="line"/>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
54 <output name="output" file="three_cluster_plot_line.pdf" ftype="pdf" compare="sim_size"/>
6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
parents: 77
diff changeset
55 </test>
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
56 </tests>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
57 <help><![CDATA[
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
58
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
59 This tool plots the coverage over a specified region (by default all chromosomes/contigs).
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
60
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
61 ]]></help>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
62 </tool>