Mercurial > repos > mvdbeek > bam_readtagger

annotate plot_coverage.xml @ 39:432bb619c079 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 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
author mvdbeek
date Thu, 15 Mar 2018 07:20:58 -0400
parents f6311a04a6c9
children 4b1ebfcd0f46
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
38
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
parents: 37
diff changeset
1 <tool id="plot_coverage" name="Plot coverage" version="0.4.9">
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>
38
f6311a04a6c9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
mvdbeek
parents: 37
diff changeset
4 <requirement type="package" version="0.4.9">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[
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
7 #import re
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
8 #set identifier1 = re.sub('[^\w\-_\.\,]', '_', str( $input1.element_identifier))
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
9 #set identifier2 = re.sub('[^\w\-_\.\,]', '_', str( $input2.element_identifier))
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
10 plot_coverage '$input1' '$identifier1' '$input2' '$identifier2' output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions'
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
11 ]]></command>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
12 <inputs>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
13 <param name="input1" type="data" format="bam,cram" label="Select a BAM file to plot"/>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
14 <param name="input2" type="data" format="bam,cram" label="Select a second BAM file to plot" optional="true"/>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
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.">
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
16 <sanitizer>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
17 <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
18 <add value="-" />
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
19 <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
20 <add value=":" />
34
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
21 </valid>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
22 </sanitizer>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
23 </param>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
24 </inputs>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
25 <outputs>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
26 <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
27 </outputs>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
28 <tests>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
29 <test>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
30 <param name="input1" value="three_cluster_out.bam" ftype="bam"/>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
31 <param name="input2" value="three_cluster_out.bam" ftype="bam"/>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
32 <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
33 <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
34 </test>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
35 </tests>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
36 <help><![CDATA[
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
37
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
38 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
39
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
40 ]]></help>
240c901dedc0 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
diff changeset
41 </tool>