Mercurial > repos > mvdbeek > bam_readtagger

annotate plot_coverage.xml @ 76:8c3d8d38674a draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit fee3f43c26cd13ffdb81d64a3c7809c570ba2194"
author mvdbeek
date Mon, 23 Mar 2020 12:42:34 -0400
parents 2c7f70390b7c
children b9b76f9a816c
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76
8c3d8d38674a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit fee3f43c26cd13ffdb81d64a3c7809c570ba2194"
mvdbeek
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1 <tool id="plot_coverage" name="Plot coverage" version="0.5.23">
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2 <description>as area plot between BAM files</description>
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="0.5.23">readtagger</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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mvdbeek
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7 #import re
2c7f70390b7c "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
mvdbeek
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8 plot_coverage
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mvdbeek
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9 #for $r in $input_files
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10 #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier))
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mvdbeek
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11 --file '$r.input' '$identifier' $r.total_reads
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12 #end for
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13 output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions'
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14 ]]></command>
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15 <inputs>
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mvdbeek
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16 <repeat name="input_files" title="Add input files to coverage plot" min="1">
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mvdbeek
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17 <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/>
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mvdbeek
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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
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19 </repeat>
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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.">
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21 <sanitizer>
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22 <valid initial="string.letters,string.digits">
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23 <add value="-" />
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24 <add value="," />
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25 <add value=":" />
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26 </valid>
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27 </sanitizer>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
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36 <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"
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37 <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
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38 <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
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39 <param name="regions" value="3R:13373525-13373615"/>
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40 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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45 This tool plots the coverage over a specified region (by default all chromosomes/contigs).
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47 ]]></help>
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48 </tool>