Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 2:18e36ab5e669 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 08:05:41 -0400
parents 8b80357d8ab1
children f44435b6ad19
comparison
equal deleted inserted replaced
1:8b80357d8ab1 2:18e36ab5e669
21 <configfiles> 21 <configfiles>
22 <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey 22 <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey
23 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 23 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
24 <Session genome="${genome}" hasGeneTrack="true" hasSequenceTrack="true" version="8"> 24 <Session genome="${genome}" hasGeneTrack="true" hasSequenceTrack="true" version="8">
25 <Resources> 25 <Resources>
26 #import os
26 #for $inputsection in $inputfiles 27 #for $inputsection in $inputfiles
27 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension) 28 #set $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension))
28 <Resource name="$inputsection.input.element_identifier" path="$path"/> 29 #set $coverage_id="%s_coverage" % $path
30 <Resource path="$path"/>
29 #end for 31 #end for
30 </Resources> 32 </Resources>
31 #for $inputsection in $inputfiles 33 #for $inputsection in $inputfiles
32 #if $inputsection.input.is_of_type('bam') 34 #if $inputsection.input.is_of_type('bam')
33 #set $label=$inputsection.label if not $inputsection.label == '' else $inputsection.input.element_identifier 35 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
34 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension) 36 #set $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension))
35 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width"> 37 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
36 ## First track is the coverage 38 ## First track is the coverage
37 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="${label}_coverage" name="${label} Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true"> 39 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
38 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/> 40 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
39 </Track> 41 </Track>
40 ## Second track is the actual BAM alignment file 42 ## Second track is the actual BAM alignment file
41 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="label" sortable="true" visible="true"> 43 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" sortable="true" visible="true">
42 <RenderOptions colorByTag="$inputsection.color_by_tag" colorOption="TAG" flagUnmappedPairs="false" groupByOption="NONE" groupByTag="BR" linkByTag="READNAME" linkedReads="false" maxInsertSize="1000" minInsertSize="50" quickConsensusMode="false" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag="" viewPairs="false"/> 44 <RenderOptions colorByTag="$inputsection.color_by_tag" colorOption="TAG" flagUnmappedPairs="false" groupByOption="NONE" groupByTag="BR" linkByTag="READNAME" linkedReads="false" maxInsertSize="1000" minInsertSize="50" quickConsensusMode="false" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag="" viewPairs="false"/>
43 </Track> 45 </Track>
44 </Panel> 46 </Panel>
45 #end if 47 #end if
46 #end for 48 #end for
49 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;817.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" height="35" id="${genome}_genes" name="Gene" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"> 51 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;817.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" height="35" id="${genome}_genes" name="Gene" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count">
50 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="817.0" minimum="0.0" type="LINEAR"/> 52 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="817.0" minimum="0.0" type="LINEAR"/>
51 </Track> 53 </Track>
52 #for $inputsection in $inputfiles 54 #for $inputsection in $inputfiles
53 #if not $inputsection.input.is_of_type('bam') 55 #if not $inputsection.input.is_of_type('bam')
54 #set $label=$inputsection.label if not $inputsection.label == '' else $inputsection.input.element_identifier 56 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
55 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension) 57 #set $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension))
56 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="${path}" name="${label}" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/> 58 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
57 #end if 59 #end if
58 #end for 60 #end for
59 </Panel> 61 </Panel>
60 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/> 62 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
61 </Session> 63 </Session>
67 exit 69 exit
68 </configfile> 70 </configfile>
69 </configfiles> 71 </configfiles>
70 <inputs> 72 <inputs>
71 <repeat name="inputfiles" min="1" title="Add tracks"> 73 <repeat name="inputfiles" min="1" title="Add tracks">
72 <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file"/> 74 <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file">
75 <validator type="unspecified_build" />
76 </param>
73 <param name="label" type="text" label="Enter a label for this file. If no label is entered the history name will be used"/> 77 <param name="label" type="text" label="Enter a label for this file. If no label is entered the history name will be used"/>
74 <param name="section_height" type="integer" value="300" label="Height for this track"/> 78 <param name="section_height" type="integer" value="300" label="Height for this track"/>
75 <param name="color_by_tag" type="text" value="CD" label="Enter a BAM/SAM tag that should detrmine the color of a read"> 79 <param name="color_by_tag" type="text" value="CD" label="Enter a BAM/SAM tag that should detrmine the color of a read">
76 <sanitizer invalid_char=""> 80 <sanitizer invalid_char="">
77 <valid initial="string.letters,string.digits"><add value="_" /> </valid> 81 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
78 </sanitizer> 82 </sanitizer>
79 </param> 83 </param>
80 </repeat> 84 </repeat>
81 <param name="script_file" type="data" format="text" label="Select a IGV script with regions for which to take screenshots"/> 85 <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/>
82 <param name="width" label="Select the screenshot width" type="integer" min="640" value="1080"/> 86 <param name="width" label="Select the screenshot width" type="integer" min="640" value="1080"/>
83 <param name="height" label="Select the screenshot height" type="integer" min="800" value="1920"/> 87 <param name="height" label="Select the screenshot height" type="integer" min="800" value="1920"/>
84 </inputs> 88 </inputs>
85 <outputs> 89 <outputs>
86 <data name="igv_session_out" format="xml"/> 90 <data name="igv_session_out" format="xml"/>