Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 3:f44435b6ad19 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 08:46:22 -0400
parents 18e36ab5e669
children a4877f60773a
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2:18e36ab5e669 3:f44435b6ad19
3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement> 3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
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 #set $abspath=os.path.abspath($path)
9 sed -i.bak -e 's|$path|$abspath|g' '$igv_session' &&
8 ln -fs $inputsection.input $path && 10 ln -fs $inputsection.input $path &&
9 #if $inputsection.input.is_of_type('bam') 11 #if $inputsection.input.is_of_type('bam')
10 ln -fs $inputsection.input.metadata.bam_index '$path'.bai && 12 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
11 #end if 13 #end if
12 #end for 14 #end for
21 <configfiles> 23 <configfiles>
22 <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey 24 <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey
23 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 25 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
24 <Session genome="${genome}" hasGeneTrack="true" hasSequenceTrack="true" version="8"> 26 <Session genome="${genome}" hasGeneTrack="true" hasSequenceTrack="true" version="8">
25 <Resources> 27 <Resources>
26 #import os
27 #for $inputsection in $inputfiles 28 #for $inputsection in $inputfiles
28 #set $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)) 29 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
29 #set $coverage_id="%s_coverage" % $path 30 #set $coverage_id="%s_coverage" % $path
30 <Resource path="$path"/> 31 <Resource path="$path"/>
31 #end for 32 #end for
32 </Resources> 33 </Resources>
33 #for $inputsection in $inputfiles 34 #for $inputsection in $inputfiles
34 #if $inputsection.input.is_of_type('bam') 35 #if $inputsection.input.is_of_type('bam')
35 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier) 36 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
36 #set $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)) 37 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
37 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width"> 38 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
38 ## First track is the coverage 39 ## First track is the coverage
39 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true"> 40 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
40 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/> 41 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
41 </Track> 42 </Track>
52 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="817.0" minimum="0.0" type="LINEAR"/> 53 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="817.0" minimum="0.0" type="LINEAR"/>
53 </Track> 54 </Track>
54 #for $inputsection in $inputfiles 55 #for $inputsection in $inputfiles
55 #if not $inputsection.input.is_of_type('bam') 56 #if not $inputsection.input.is_of_type('bam')
56 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier) 57 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
57 #set $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)) 58 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
58 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/> 59 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
59 #end if 60 #end if
60 #end for 61 #end for
61 </Panel> 62 </Panel>
62 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/> 63 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>