Mercurial > repos > mvdbeek > bam_readtagger
diff plot_coverage.xml @ 75:2c7f70390b7c draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"
| author | mvdbeek |
|---|---|
| date | Mon, 23 Mar 2020 10:24:02 -0400 |
| parents | 6c15dd4415ea |
| children | 8c3d8d38674a |
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--- a/plot_coverage.xml Mon Jan 13 10:10:10 2020 -0500 +++ b/plot_coverage.xml Mon Mar 23 10:24:02 2020 -0400 @@ -1,17 +1,22 @@ -<tool id="plot_coverage" name="Plot coverage" version="0.5.21"> +<tool id="plot_coverage" name="Plot coverage" version="0.5.22"> <description>as area plot between BAM files</description> <requirements> - <requirement type="package" version="0.5.21">readtagger</requirement> + <requirement type="package" version="0.5.22">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' +#import re +plot_coverage +#for $r in $input_files + #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier)) + --file '$r.input' '$identifier' $r.total_reads +#end for +output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$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"/> + <repeat name="input_files" title="Add input files to coverage plot" min="1"> + <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/> + <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"/> + </repeat> <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"> @@ -27,8 +32,10 @@ </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="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/> + <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/> + <param name="input_files_0|total_reads" value="1000000" ftype="bam"/> + <param name="input_files_1|total_reads" value="1000000" ftype="bam"/> <param name="regions" value="3R:13373525-13373615"/> <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/> </test>