Mercurial > repos > mvdbeek > bam_readtagger
comparison plot_coverage.xml @ 37:73e3060d104f draft
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 |
| parents | |
| children | 700df574a69c |
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| 36:e19ff7992765 | 37:73e3060d104f |
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| 1 <tool id="plot_coverage" name="Plot coverage" version="0.4.1"> | |
| 2 <description>as area plot between BAM files</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.4.1">readtagger</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="aggressive"><![CDATA[ | |
| 7 #import re | |
| 8 #set identifier1 = re.sub('[^\w\-_\.\,]', '_', str( $input1.element_identifier)) | |
| 9 #set identifier2 = re.sub('[^\w\-_\.\,]', '_', str( $input2.element_identifier)) | |
| 10 plot_coverage '$input1' '$identifier1' '$input2' '$identifier2' output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' | |
| 11 ]]></command> | |
| 12 <inputs> | |
| 13 <param name="input1" type="data" format="bam,cram" label="Select a BAM file to plot"/> | |
| 14 <param name="input2" type="data" format="bam,cram" label="Select a second BAM file to plot" optional="true"/> | |
| 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."> | |
| 16 <sanitizer> | |
| 17 <valid initial="string.letters,string.digits"> | |
| 18 <add value="-" /> | |
| 19 <add value="," /> | |
| 20 </valid> | |
| 21 </sanitizer> | |
| 22 </param> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
| 29 <param name="input1" value="three_cluster_out.bam" ftype="bam"/> | |
| 30 <param name="input2" value="three_cluster_out.bam" ftype="bam"/> | |
| 31 <param name="regions" value="3R:13373525-13373615"/> | |
| 32 <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/> | |
| 33 </test> | |
| 34 </tests> | |
| 35 <help><![CDATA[ | |
| 36 | |
| 37 This tool plots the coverage over a specified region (by default all chromosomes/contigs). | |
| 38 | |
| 39 ]]></help> | |
| 40 </tool> |