Mercurial > repos > artbio > probecoverage

comparison probecoverage.xml @ 3:4f744d3aaf0b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 8159fa0b4667a953c05aca50d412c33e619b5080
author artbio
date Sun, 24 Sep 2017 14:47:11 -0400
parents 35d2db3753d9
children daec4df60281
comparison
equal deleted inserted replaced
2:35d2db3753d9 3:4f744d3aaf0b
1 <tool id="probecoverage" name="Probe Coverage" version="0.3.0"> 1 <tool id="probecoverage" name="Probe Coverage" version="0.4.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4.1">samtools</requirement> 4 <requirement type="package" version="1.4.1">samtools</requirement>
5 <requirement type="package" version="2.26.0">bedtools</requirement> 5 <requirement type="package" version="2.26.0">bedtools</requirement>
6 <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement> 6 <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>
24 #for $file in $inputs 24 #for $file in $inputs
25 '$file' 25 '$file'
26 #end for 26 #end for
27 -bed '$bed' > $coverage_dataframe && 27 -bed '$bed' > $coverage_dataframe &&
28 Rscript '$__tool_directory__'/probecoverage.r 28 Rscript '$__tool_directory__'/probecoverage.r
29 --method '$method'
29 --input '$coverage_dataframe' 30 --input '$coverage_dataframe'
30 --title 'Probe coverage depth (cumulative distribution)' 31 --title 'Probe coverage depth (cumulative distribution)'
31 --xlab 32 --xlab
32 #if $method == 'pysam': 33 #if $method == 'pysam':
33 'Depth (pysam method)' 34 'Depth (pysam method)'