Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 8:ff0fb6dde58e 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 10:58:06 -0400
parents 755832a07414
children c357862a2927
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7:755832a07414 8:ff0fb6dde58e
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
14 ln -fs $igv_session igv_session.xml && 14 ln -fs $igv_session igv_session.xml &&
15 cat '$load_session' > load_session.txt && 15 cat '$load_session' > load_session.txt &&
16 echo snapshotDirectory "\$PWD" >> load_session.txt && 16 echo snapshotDirectory "\$PWD" >> load_session.txt &&
17 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt && 17 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
18 sleep 10s &&
18 python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height && 19 python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height &&
19 cp '$igv_session' '$igv_session_out' && 20 cp '$igv_session' '$igv_session_out' &&
20 zip screenshots.zip *.png && 21 zip screenshots.zip *.png &&
21 cp screenshots.zip '$screenshots_out' 22 cp screenshots.zip '$screenshots_out'
22 ]]></command> 23 ]]></command>