Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 0:d828cf6bff42 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, 26 Jun 2017 10:00:06 -0400
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children 8b80357d8ab1
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-1:000000000000 0:d828cf6bff42
1 <tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 #for $inputsection in $inputfiles
7 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
8 ln -fs $inputsection.input $path &&
9 #if $inputsection.input.is_of_type('bam')
10 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
11 #end if
12 #end for
13 cat '$load_session' > load_session.txt &&
14 echo snapshotDirectory "\$PWD" >> load_session.txt &&
15 cat load_session.txt '$script_file' '$exit_session' > '$igv_session_out' &&
16 python $__tool_directory__/xvfb_igv.py '$igv_session_out' $width,$height &&
17 zip '$screenshots_out' *.png
18 ]]></command>
19 <configfiles>
20 <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey
21 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
22 <Session genome="${genome}" hasGeneTrack="true" hasSequenceTrack="true" version="8">
23 <Resources>
24 #for $inputsection in $inputfiles
25 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
26 <Resource name="$inputsection.input.element_identifier" path="$path"/>
27 #end for
28 </Resources>
29 #for $inputsection in $inputfiles
30 #if $inputsection.input.is_of_type('bam')
31 #set $label=$inputsection.label if not $inputsection.label == '' else $inputsection.input.element_identifier
32 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
33 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
34 ## First track is the coverage
35 <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">
36 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
37 </Track>
38 ## Second track is the actual BAM alignment file
39 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="label" sortable="true" visible="true">
40 <RenderOptions colorByTag="$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"/>
41 </Track>
42 </Panel>
43 #end if
44 #end for
45 <Panel height="186" name="FeaturePanel" width="$width">
46 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="Reference sequence" name="Reference sequence" sortable="false" visible="true"/>
47 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;817.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" height="35" id="${genome}_genes" name="Gene" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count">
48 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="817.0" minimum="0.0" type="LINEAR"/>
49 </Track>
50 #for $inputsection in $inputfiles
51 #if not $inputsection.input.is_of_type('bam')
52 #set $label=$inputsection.label if not $inputsection.label == '' else $inputsection.input.element_identifier
53 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
54 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="${path}" name="${label}" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
55 #end if
56 #end for
57 </Panel>
58 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
59 </Session>
60 ]]></configfile>
61 <configfile name="load_session">
62 load $igv_session
63 </configfile>
64 <configfile name="exit_session">
65 exit
66 </configfile>
67 </configfiles>
68 <inputs>
69 <repeat name="inputfiles" min="1" title="Add tracks">
70 <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file"/>
71 <param name="label" type="text" label="Enter a label for this file. If no label is entered the history name will be used"/>
72 <param name="section_height" type="integer" value="300" label="Height for this track"/>
73 <param name="color_by_tag" type="text" value="CD" label="Enter a BAM/SAM tag that should detrmine the color of a read">
74 <sanitizer invalid_char="">
75 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
76 </sanitizer>
77 </param>
78 </repeat>
79 <param name="script_file" type="data" format="text" label="Select a IGV script with regions for which to take screenshots"/>
80 <param name="width" label="Select the screenshot width" type="integer" min="640" value="1080"/>
81 <param name="height" label="Select the screenshot height" type="integer" min="800" value="1920"/>
82 </inputs>
83 <outputs>
84 <data name="igv_session_out" format="xml"/>
85 <data name="screenshots_out" format="zip"/>
86 </outputs>
87 <help><![CDATA[
88 TODO: Fill in help.
89 ]]></help>
90 </tool>