Mercurial > repos > mvdbeek > bam_readtagger

annotate plot_coverage.xml @ 70:94731adae3e4 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 8ee42193ec9c4778fd2bd312f53322389b0731c5"
author mvdbeek
date Mon, 23 Mar 2020 14:23:31 +0000
parents 44f5ed2c9a26
children 156c4b5f3f38
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
70
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
1 <tool id="plot_coverage" name="Plot coverage" version="0.5.22">
37
73e3060d104f 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>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
3 <requirements>
70
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
4 <requirement type="package" version="0.5.22">readtagger</requirement>
37
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
5 </requirements>
73e3060d104f 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[
70
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
7 #import re
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
8 plot_coverage
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
9 #for $r in $input_files
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
10 #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier))
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
11 --file '$r.input' '$identifier' $r.total_reads
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
12 #end for
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions'
37
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
14 ]]></command>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
15 <inputs>
70
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
16 <repeat name="input_files" title="Add input files to coverage plot" min="1">
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
17 <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/>
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
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"/>
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
19 </repeat>
37
73e3060d104f 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.">
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
21 <sanitizer>
73e3060d104f 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">
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
23 <add value="-" />
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
24 <add value="," />
41
29734dbad6de planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2e991a52c828b0234020e89748eafe1028e44a7d
mvdbeek
parents: 40
diff changeset
25 <add value=":" />
37
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
26 </valid>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
27 </sanitizer>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
28 </param>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
29 </inputs>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
30 <outputs>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
31 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
32 </outputs>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
33 <tests>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
34 <test>
70
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
35 <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
36 <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/>
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
37 <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
94731adae3e4 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
parents: 69
diff changeset
38 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
37
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
39 <param name="regions" value="3R:13373525-13373615"/>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
40 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
41 </test>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
42 </tests>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
43 <help><![CDATA[
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
44
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
45 This tool plots the coverage over a specified region (by default all chromosomes/contigs).
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
46
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
47 ]]></help>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
48 </tool>