Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 13:1100d5a77c4d draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1ddb87e95baeea2a4ee9b95930da6e0927fb7ff7-dirty
author mvdbeek
date Fri, 28 Jul 2017 12:47:05 -0400
parents 9dca6aa224a2
children 9663fa8b9c0b
comparison
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12:9dca6aa224a2 13:1100d5a77c4d
1 <tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.0"> 1 <tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement> 3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
4 <requirement type="package" version="2.3.93">igv</requirement>
4 </requirements> 5 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
6 #for $inputsection in $inputfiles 7 ln -s '$genome_source.genome' genome.fa &&
7 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension) 8 samtools faidx genome.fa &&
8 sed -i.bak -e "s|$path|\$PWD/$path|g" '$igv_session' && 9 sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' &&
10 #for $i, $inputsection in enumerate($inputfiles):
11 #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
12 sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" '$igv_session' &&
9 ln -fs '$inputsection.input' '$path' && 13 ln -fs '$inputsection.input' '$path' &&
10 #if $inputsection.input.is_of_type('bam') 14 #if $inputsection.input.is_of_type('bam')
11 ln -fs $inputsection.input.metadata.bam_index '$path'.bai && 15 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
12 #end if 16 #end if
13 #end for 17 #end for
14 ln -fs $igv_session igv_session.xml && 18 ln -fs $igv_session igv_session.xml &&
15 cat '$load_session' > load_session.txt && 19 cat '$load_session' > load_session.txt &&
16 echo snapshotDirectory "\$PWD" >> load_session.txt && 20 echo snapshotDirectory "\$PWD" >> load_session.txt &&
17 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt && 21 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
18 ## gives the cluster a bit of time to actually create the symlinks ... ughs 22 cp '$igv_session' '$igv_session_out' &&
19 sleep 10s &&
20 python $__tool_directory__/xvfb_igv.py igv_script.txt '$igv_preferences' $width,$height && 23 python $__tool_directory__/xvfb_igv.py igv_script.txt '$igv_preferences' $width,$height &&
21 cp '$igv_session' '$igv_session_out' &&
22 zip screenshots.zip *.png && 24 zip screenshots.zip *.png &&
23 cp screenshots.zip '$screenshots_out' 25 cp screenshots.zip '$screenshots_out'
24 ]]></command> 26 ]]></command>
25 <configfiles> 27 <configfiles>
26 <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey 28 <configfile name="igv_session"><![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
27 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 29 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8">
28 <Session genome="${genome}" hasGeneTrack="true" hasSequenceTrack="true" version="8">
29 <Resources> 30 <Resources>
30 #for $inputsection in $inputfiles 31 #for $i, $inputsection in enumerate($inputfiles):
31 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension) 32 #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
32 #set $coverage_id="%s_coverage" % $path 33 #set $coverage_id="%s_coverage" % $path
33 <Resource path="$path"/> 34 <Resource path="$path"/>
34 #end for 35 #end for
35 </Resources> 36 </Resources>
36 #for $inputsection in $inputfiles 37 #for $i, $inputsection in enumerate($inputfiles):
37 #if $inputsection.input.is_of_type('bam') 38 #if $inputsection.input.is_of_type('bam')
38 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier) 39 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
39 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension) 40 #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
40 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width"> 41 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
41 ## First track is the coverage 42 ## First track is the coverage
42 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true"> 43 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
43 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/> 44 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
44 </Track> 45 </Track>
49 </Panel> 50 </Panel>
50 #end if 51 #end if
51 #end for 52 #end for
52 <Panel height="186" name="FeaturePanel" width="$width"> 53 <Panel height="186" name="FeaturePanel" width="$width">
53 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="Reference sequence" name="Reference sequence" sortable="false" visible="true"/> 54 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="Reference sequence" name="Reference sequence" sortable="false" visible="true"/>
54 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;817.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" height="35" id="${genome}_genes" name="Gene" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"> 55 #for $i, $inputsection in enumerate($inputfiles):
55 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="817.0" minimum="0.0" type="LINEAR"/>
56 </Track>
57 #for $inputsection in $inputfiles
58 #if not $inputsection.input.is_of_type('bam') 56 #if not $inputsection.input.is_of_type('bam')
59 #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)
60 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension) 58 #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
61 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$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="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
62 #end if 60 #end if
63 #end for 61 #end for
64 </Panel> 62 </Panel>
65 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/> 63 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
74 <configfile name="igv_preferences"> 72 <configfile name="igv_preferences">
75 SAM.SHOW_SOFT_CLIPPED=$show_softclippped 73 SAM.SHOW_SOFT_CLIPPED=$show_softclippped
76 </configfile> 74 </configfile>
77 </configfiles> 75 </configfiles>
78 <inputs> 76 <inputs>
77 <conditional name="genome_source">
78 <param name="input_type_selector" type="select" label="Choose the genome source">
79 <option value="cached" selected="True">Built-in references</option>
80 <option value="history">Select a fasta file from your history</option>
81 </param>
82 <when value="cached">
83 <param name="genome" type="select" label="Select a genome">
84 <options from_data_table="fasta_indexes" />
85 </param>
86 </when>
87 <when value="history">
88 <param name="genome" type="data" format="fasta" label="Select a fasta file as reference genome"/>
89 </when>
90 </conditional>
79 <repeat name="inputfiles" min="1" title="Add tracks"> 91 <repeat name="inputfiles" min="1" title="Add tracks">
80 <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file"> 92 <param name="input" type="data" format="bam,gff,gff3,gtf,bed,vcf" label="Choose an input file"/>
81 <validator type="unspecified_build" />
82 </param>
83 <param name="label" type="text" label="Enter a label for this file. If no label is entered the history name will be used"/> 93 <param name="label" type="text" label="Enter a label for this file. If no label is entered the history name will be used"/>
84 <param name="section_height" type="integer" value="300" label="Height for this track"/> 94 <param name="section_height" type="integer" value="300" label="Height for this track"/>
85 <param name="color_by_tag" type="text" value="CD" label="Enter a BAM/SAM tag that should detrmine the color of a read"> 95 <param name="color_by_tag" type="text" value="CD" label="Enter a BAM/SAM tag that should detrmine the color of a read">
86 <sanitizer invalid_char=""> 96 <sanitizer invalid_char="">
87 <valid initial="string.letters,string.digits"><add value="_" /> </valid> 97 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
95 </inputs> 105 </inputs>
96 <outputs> 106 <outputs>
97 <data name="igv_session_out" format="xml"/> 107 <data name="igv_session_out" format="xml"/>
98 <data name="screenshots_out" format="zip"/> 108 <data name="screenshots_out" format="zip"/>
99 </outputs> 109 </outputs>
110 <tests>
111 <test>
112 <param name="genome_source|input_type_selector" value="history"/>
113 <param name="genome_source|genome" value="rover_reference.fa"/>
114 <repeat name="inputfiles">
115 <param name="input" value="rover_corrected.bam"/>
116 </repeat>
117 <output name="igv_session_out" file="igv_session.xml" lines_diff="6"/>
118 </test>
119 </tests>
100 <help><![CDATA[ 120 <help><![CDATA[
101 TODO: Fill in help. 121 This tool can automate taking screenshots using IGV.
122 It takes as input a reference genome, an IGV script file (bedtools igv can produce such a file)
123 and a variable number of BAM,GFF,GTF,BED or VCF files, and produces a zip file containing screenshots for each genomic region in the IGV script file.
102 ]]></help> 124 ]]></help>
125 <citations>
126 <citation type="doi">10.1093/bib/bbs017</citation>
127 </citations>
103 </tool> 128 </tool>