Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 6:54bc6c6d667c draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
author mvdbeek
date Mon, 03 Jul 2017 08:53:28 -0400
parents 20cc4cc902f4
children 755832a07414
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5:20cc4cc902f4 6:54bc6c6d667c
3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement> 3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 #for $inputsection in $inputfiles 6 #for $inputsection in $inputfiles
7 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension) 7 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
8 sed -i.bak -e 's|$path|\$PWD/$path|g' '$igv_session' && 8 sed -i.bak -e "s|$path|\$PWD/$path|g" '$igv_session' &&
9 ln -fs $inputsection.input $path && 9 ln -fs $inputsection.input $path &&
10 #if $inputsection.input.is_of_type('bam') 10 #if $inputsection.input.is_of_type('bam')
11 ln -fs $inputsection.input.metadata.bam_index '$path'.bai && 11 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
12 #end if 12 #end if
13 #end for 13 #end for