Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 20:1f8609ae3941 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit be45e3b0dec4ca1e8611abb2d84dd995e6d53751-dirty
author mvdbeek
date Mon, 31 Jul 2017 12:45:19 -0400
parents fd2d19ae2648
children de2f2c28c498
comparison
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19:fd2d19ae2648 20:1f8609ae3941
1 <tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.0"> 1 <tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.1">
2 <macros>
3 <token name="@PATH@"><![CDATA[#set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)]]></token>
4 </macros>
5 <requirements> 2 <requirements>
6 <requirement type="package" version="0.2.9">xvfbwrapper</requirement> 3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
7 <requirement type="package" version="2.3.93">igv</requirement> 4 <requirement type="package" version="2.3.93">igv</requirement>
8 </requirements> 5 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
14 ln -s '$genome_source.genome.fields.path' genome.fa && 11 ln -s '$genome_source.genome.fields.path' genome.fa &&
15 #end if 12 #end if
16 samtools faidx genome.fa && 13 samtools faidx genome.fa &&
17 sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' && 14 sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' &&
18 #for $i, $inputsection in enumerate($inputfiles): 15 #for $i, $inputsection in enumerate($inputfiles):
19 @PATH@ 16 #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)
20 sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" '$igv_session' && 17 sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" '$igv_session' &&
21 ln -fs '$inputsection.input' '$path' && 18 ln -fs '$inputsection.input' '$path' &&
22 #if $inputsection.input.is_of_type('bam') 19 #if $inputsection.input.is_of_type('bam')
23 ln -fs $inputsection.input.metadata.bam_index '$path'.bai && 20 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
24 #end if 21 #end if
36 <configfile name="igv_session">#import re 33 <configfile name="igv_session">#import re
37 <![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?> 34 <![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
38 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8"> 35 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8">
39 <Resources> 36 <Resources>
40 #for $i, $inputsection in enumerate($inputfiles): 37 #for $i, $inputsection in enumerate($inputfiles):
41 @PATH@ 38 #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)
42 #set $coverage_id="%s_coverage" % $path 39 #set $coverage_id="%s_coverage" % $path
43 <Resource path="$path"/> 40 <Resource path="$path"/>
44 #end for 41 #end for
45 </Resources> 42 </Resources>
46 #for $i, $inputsection in enumerate($inputfiles): 43 #for $i, $inputsection in enumerate($inputfiles):
47 #if $inputsection.input.is_of_type('bam') 44 #if $inputsection.input.is_of_type('bam')
48 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier) 45 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
49 @PATH 46 #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)
50 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width"> 47 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
51 ## First track is the coverage 48 ## First track is the coverage
52 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true"> 49 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
53 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/> 50 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
54 </Track> 51 </Track>
62 <Panel height="186" name="FeaturePanel" width="$width"> 59 <Panel height="186" name="FeaturePanel" width="$width">
63 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="Reference sequence" name="Reference sequence" sortable="false" visible="true"/> 60 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="Reference sequence" name="Reference sequence" sortable="false" visible="true"/>
64 #for $i, $inputsection in enumerate($inputfiles): 61 #for $i, $inputsection in enumerate($inputfiles):
65 #if not $inputsection.input.is_of_type('bam') 62 #if not $inputsection.input.is_of_type('bam')
66 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier) 63 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
67 @PATH@ 64 #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)
68 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/> 65 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
69 #end if 66 #end if
70 #end for 67 #end for
71 </Panel> 68 </Panel>
72 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/> 69 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>