Mercurial > repos > mvdbeek > bam_readtagger
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_coverage.xml Mon Nov 20 10:50:23 2017 -0500 @@ -0,0 +1,40 @@ +<tool id="plot_coverage" name="Plot coverage" version="0.4.1"> + <description>as area plot between BAM files</description> + <requirements> + <requirement type="package" version="0.4.1">readtagger</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + #import re + #set identifier1 = re.sub('[^\w\-_\.\,]', '_', str( $input1.element_identifier)) + #set identifier2 = re.sub('[^\w\-_\.\,]', '_', str( $input2.element_identifier)) + plot_coverage '$input1' '$identifier1' '$input2' '$identifier2' output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' + ]]></command> + <inputs> + <param name="input1" type="data" format="bam,cram" label="Select a BAM file to plot"/> + <param name="input2" type="data" format="bam,cram" label="Select a second BAM file to plot" optional="true"/> + <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."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="-" /> + <add value="," /> + </valid> + </sanitizer> + </param> + </inputs> + <outputs> + <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/> + </outputs> + <tests> + <test> + <param name="input1" value="three_cluster_out.bam" ftype="bam"/> + <param name="input2" value="three_cluster_out.bam" ftype="bam"/> + <param name="regions" value="3R:13373525-13373615"/> + <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + +This tool plots the coverage over a specified region (by default all chromosomes/contigs). + + ]]></help> +</tool>