Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 28:d6541171175c draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0437e9e56f0af2ccfb5f119b0f290109807ed9b0-dirty
author mvdbeek
date Fri, 15 Jun 2018 13:11:56 -0400
parents 676591c44f64
children dd61761307ca
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27:676591c44f64 28:d6541171175c
16 <!-- TODO: uncomment when igv in conda 16 <!-- TODO: uncomment when igv in conda
17 <requirement type="package" version="2.3.93">igv</requirement> 17 <requirement type="package" version="2.3.93">igv</requirement>
18 --> 18 -->
19 </requirements> 19 </requirements>
20 <command detect_errors="exit_code"><![CDATA[ 20 <command detect_errors="exit_code"><![CDATA[
21 #import re
22 #if $genome_source.input_type_selector == 'history': 21 #if $genome_source.input_type_selector == 'history':
23 ln -s '$genome_source.genome' genome.fa && 22 ln -s '$genome_source.genome' genome.fa &&
24 #else: 23 #else:
25 ln -s '$genome_source.genome.fields.path' genome.fa && 24 ln -s '$genome_source.genome.fields.path' genome.fa &&
26 #end if 25 #end if
43 zip screenshots.zip *.png && 42 zip screenshots.zip *.png &&
44 cp screenshots.zip '$screenshots_out' 43 cp screenshots.zip '$screenshots_out'
45 #end if 44 #end if
46 ]]></command> 45 ]]></command>
47 <configfiles> 46 <configfiles>
48 <configfile name="igv_session"> 47 <configfile name="igv_session"><![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
49 <![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
50 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8"> 48 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8">
51 <Resources> 49 <Resources>
52 #for $i, $inputsection in enumerate($inputfiles): 50 #for $i, $inputsection in enumerate($inputfiles):
53 @PATH@ 51 @PATH@
54 #set $coverage_id="%s_coverage" % $path 52 #set $coverage_id="%s_coverage" % $path
82 #end for 80 #end for
83 </Panel> 81 </Panel>
84 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/> 82 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
85 </Session> 83 </Session>
86 ]]></configfile> 84 ]]></configfile>
87 <configfile name="igv_session_remote"> 85 <configfile name="igv_session_remote"><![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
88 <![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
89 <Session genome="dm6" hasGeneTrack="true" hasSequenceTrack="true" version="8"> 86 <Session genome="dm6" hasGeneTrack="true" hasSequenceTrack="true" version="8">
90 <Resources>#for $i, $inputsection in enumerate($inputfiles):@DISPLAY_LINK@<Resource path="$display_link"/>#end for 87 <Resources>#for $i, $inputsection in enumerate($inputfiles):@DISPLAY_LINK@<Resource path="$display_link"/>#end for
91 </Resources> 88 </Resources>
92 #for $i, $inputsection in enumerate($inputfiles): 89 #for $i, $inputsection in enumerate($inputfiles):
93 #if $inputsection.input.is_of_type('bam') 90 #if $inputsection.input.is_of_type('bam')