Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 11:64eb1ffd7872 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 12:10:06 -0400
parents afb3f4c224d4
children 9dca6aa224a2
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10:afb3f4c224d4 11:64eb1ffd7872
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 ## gives the cluster a bit of time to actually create the symlinks ... ughs 18 ## gives the cluster a bit of time to actually create the symlinks ... ughs
19 sleep 10s && 19 sleep 10s &&
20 python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height && 20 python $__tool_directory__/xvfb_igv.py igv_script.txt '$igv_preferences' $width,$height &&
21 cp '$igv_session' '$igv_session_out' && 21 cp '$igv_session' '$igv_session_out' &&
22 zip screenshots.zip *.png && 22 zip screenshots.zip *.png &&
23 cp screenshots.zip '$screenshots_out' 23 cp screenshots.zip '$screenshots_out'
24 ]]></command> 24 ]]></command>
25 <configfiles> 25 <configfiles>
65 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/> 65 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
66 </Session> 66 </Session>
67 ]]></configfile> 67 ]]></configfile>
68 <configfile name="load_session"> 68 <configfile name="load_session">
69 load igv_session.xml 69 load igv_session.xml
70 preference SAM.SHOW_SOFT_CLIPPED str($show_softclippped)
71 </configfile> 70 </configfile>
72 <configfile name="exit_session"> 71 <configfile name="exit_session">
73 exit 72 exit
73 </configfile>
74 <configfile name="igv_preferences">
75 SAM.SHOW_SOFT_CLIPPED=str($show_softclippped)
74 </configfile> 76 </configfile>
75 </configfiles> 77 </configfiles>
76 <inputs> 78 <inputs>
77 <repeat name="inputfiles" min="1" title="Add tracks"> 79 <repeat name="inputfiles" min="1" title="Add tracks">
78 <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file"> 80 <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file">