Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 4:a4877f60773a 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 08:51:28 -0400
parents f44435b6ad19
children 20cc4cc902f4
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3:f44435b6ad19 4:a4877f60773a
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 #set $abspath=os.path.abspath($path) 8 sed -i.bak -e 's|$path|$PWD/$path|g' '$igv_session' &&
9 sed -i.bak -e 's|$path|$abspath|g' '$igv_session' &&
10 ln -fs $inputsection.input $path && 9 ln -fs $inputsection.input $path &&
11 #if $inputsection.input.is_of_type('bam') 10 #if $inputsection.input.is_of_type('bam')
12 ln -fs $inputsection.input.metadata.bam_index '$path'.bai && 11 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
13 #end if 12 #end if
14 #end for 13 #end for