Mercurial > repos > mvdbeek > bam_readtagger

annotate plot_coverage.xml @ 37:73e3060d104f draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
author mvdbeek
date Mon, 20 Nov 2017 10:50:23 -0500
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children 700df574a69c
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37
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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1 <tool id="plot_coverage" name="Plot coverage" version="0.4.1">
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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2 <description>as area plot between BAM files</description>
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mvdbeek
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="0.4.1">readtagger</requirement>
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mvdbeek
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5 </requirements>
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mvdbeek
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6 <command detect_errors="aggressive"><![CDATA[
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mvdbeek
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7 #import re
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mvdbeek
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8 #set identifier1 = re.sub('[^\w\-_\.\,]', '_', str( $input1.element_identifier))
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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9 #set identifier2 = re.sub('[^\w\-_\.\,]', '_', str( $input2.element_identifier))
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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10 plot_coverage '$input1' '$identifier1' '$input2' '$identifier2' output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions'
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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11 ]]></command>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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12 <inputs>
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mvdbeek
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13 <param name="input1" type="data" format="bam,cram" label="Select a BAM file to plot"/>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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14 <param name="input2" type="data" format="bam,cram" label="Select a second BAM file to plot" optional="true"/>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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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.">
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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16 <sanitizer>
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mvdbeek
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17 <valid initial="string.letters,string.digits">
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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18 <add value="-" />
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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19 <add value="," />
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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20 </valid>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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21 </sanitizer>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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22 </param>
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mvdbeek
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23 </inputs>
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mvdbeek
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24 <outputs>
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mvdbeek
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25 <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
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26 </outputs>
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mvdbeek
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27 <tests>
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mvdbeek
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28 <test>
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mvdbeek
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29 <param name="input1" value="three_cluster_out.bam" ftype="bam"/>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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30 <param name="input2" value="three_cluster_out.bam" ftype="bam"/>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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31 <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
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32 <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
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33 </test>
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mvdbeek
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34 </tests>
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mvdbeek
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35 <help><![CDATA[
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mvdbeek
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36
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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37 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
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38
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
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39 ]]></help>
73e3060d104f planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
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40 </tool>