Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 1:8b80357d8ab1 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, 26 Jun 2017 10:17:15 -0400
parents d828cf6bff42
children 18e36ab5e669
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0:d828cf6bff42 1:8b80357d8ab1
8 ln -fs $inputsection.input $path && 8 ln -fs $inputsection.input $path &&
9 #if $inputsection.input.is_of_type('bam') 9 #if $inputsection.input.is_of_type('bam')
10 ln -fs $inputsection.input.metadata.bam_index '$path'.bai && 10 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
11 #end if 11 #end if
12 #end for 12 #end for
13 ln -fs $igv_session igv_session.xml &&
13 cat '$load_session' > load_session.txt && 14 cat '$load_session' > load_session.txt &&
14 echo snapshotDirectory "\$PWD" >> load_session.txt && 15 echo snapshotDirectory "\$PWD" >> load_session.txt &&
15 cat load_session.txt '$script_file' '$exit_session' > '$igv_session_out' && 16 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
16 python $__tool_directory__/xvfb_igv.py '$igv_session_out' $width,$height && 17 python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height &&
18 cp '$igv_session' '$igv_session_out' &&
17 zip '$screenshots_out' *.png 19 zip '$screenshots_out' *.png
18 ]]></command> 20 ]]></command>
19 <configfiles> 21 <configfiles>
20 <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey 22 <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey
21 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 23 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
57 </Panel> 59 </Panel>
58 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/> 60 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
59 </Session> 61 </Session>
60 ]]></configfile> 62 ]]></configfile>
61 <configfile name="load_session"> 63 <configfile name="load_session">
62 load $igv_session 64 load igv_session.xml
63 </configfile> 65 </configfile>
64 <configfile name="exit_session"> 66 <configfile name="exit_session">
65 exit 67 exit
66 </configfile> 68 </configfile>
67 </configfiles> 69 </configfiles>