Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 9:c357862a2927 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 11:36:19 -0400
parents ff0fb6dde58e
children afb3f4c224d4
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8:ff0fb6dde58e 9:c357862a2927
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 ## gives the cluster a bit of time to actually create the symlinks ... ughs
18 sleep 10s && 19 sleep 10s &&
19 python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height && 20 python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height &&
20 cp '$igv_session' '$igv_session_out' && 21 cp '$igv_session' '$igv_session_out' &&
21 zip screenshots.zip *.png && 22 zip screenshots.zip *.png &&
22 cp screenshots.zip '$screenshots_out' 23 cp screenshots.zip '$screenshots_out'
64 <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"/>
65 </Session> 66 </Session>
66 ]]></configfile> 67 ]]></configfile>
67 <configfile name="load_session"> 68 <configfile name="load_session">
68 load igv_session.xml 69 load igv_session.xml
70 preference SAM.SHOW_SOFT_CLIPPED $show_softclippped
69 </configfile> 71 </configfile>
70 <configfile name="exit_session"> 72 <configfile name="exit_session">
71 exit 73 exit
72 </configfile> 74 </configfile>
73 </configfiles> 75 </configfiles>
82 <sanitizer invalid_char=""> 84 <sanitizer invalid_char="">
83 <valid initial="string.letters,string.digits"><add value="_" /> </valid> 85 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
84 </sanitizer> 86 </sanitizer>
85 </param> 87 </param>
86 </repeat> 88 </repeat>
89 <param name="show_softclippped" type="boolean" label="Show softclipped bases?" truevalue="true" falsevalue="false" checked="true"/>
87 <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/> 90 <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/>
88 <param name="width" label="Select the screenshot width" type="integer" min="640" value="1080"/> 91 <param name="width" label="Select the screenshot width" type="integer" min="800" value="1920"/>
89 <param name="height" label="Select the screenshot height" type="integer" min="800" value="1920"/> 92 <param name="height" label="Select the screenshot height" type="integer" min="640" value="1080"/>
90 </inputs> 93 </inputs>
91 <outputs> 94 <outputs>
92 <data name="igv_session_out" format="xml"/> 95 <data name="igv_session_out" format="xml"/>
93 <data name="screenshots_out" format="zip"/> 96 <data name="screenshots_out" format="zip"/>
94 </outputs> 97 </outputs>