Mercurial > repos > mvdbeek > igv_take_screenshots

annotate igv_make_screenshots.xml @ 10:afb3f4c224d4 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 11:42:19 -0400
parents c357862a2927
children 64eb1ffd7872
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1 <tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 #for $inputsection in $inputfiles
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7 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
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8 sed -i.bak -e "s|$path|\$PWD/$path|g" '$igv_session' &&
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9 ln -fs '$inputsection.input' '$path' &&
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10 #if $inputsection.input.is_of_type('bam')
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11 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
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12 #end if
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13 #end for
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14 ln -fs $igv_session igv_session.xml &&
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15 cat '$load_session' > load_session.txt &&
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16 echo snapshotDirectory "\$PWD" >> load_session.txt &&
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17 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
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18 ## gives the cluster a bit of time to actually create the symlinks ... ughs
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19 sleep 10s &&
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20 python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height &&
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21 cp '$igv_session' '$igv_session_out' &&
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22 zip screenshots.zip *.png &&
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23 cp screenshots.zip '$screenshots_out'
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24 ]]></command>
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25 <configfiles>
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26 <configfile name="igv_session"><![CDATA[#set $genome=$inputfiles[0].input.metadata.dbkey
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27 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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28 <Session genome="${genome}" hasGeneTrack="true" hasSequenceTrack="true" version="8">
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29 <Resources>
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30 #for $inputsection in $inputfiles
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31 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
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32 #set $coverage_id="%s_coverage" % $path
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33 <Resource path="$path"/>
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34 #end for
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35 </Resources>
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36 #for $inputsection in $inputfiles
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37 #if $inputsection.input.is_of_type('bam')
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38 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
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39 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
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40 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
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41 ## First track is the coverage
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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">
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43 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
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44 </Track>
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45 ## Second track is the actual BAM alignment file
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46 <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">
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47 <RenderOptions colorByTag="$inputsection.color_by_tag" colorOption="TAG" flagUnmappedPairs="false" groupByOption="NONE" groupByTag="BR" linkByTag="READNAME" linkedReads="false" maxInsertSize="1000" minInsertSize="50" quickConsensusMode="false" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag="" viewPairs="false"/>
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48 </Track>
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49 </Panel>
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50 #end if
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51 #end for
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52 <Panel height="186" name="FeaturePanel" width="$width">
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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"/>
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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">
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55 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="817.0" minimum="0.0" type="LINEAR"/>
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56 </Track>
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57 #for $inputsection in $inputfiles
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58 #if not $inputsection.input.is_of_type('bam')
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59 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
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60 #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
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61 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
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62 #end if
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63 #end for
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64 </Panel>
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65 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
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66 </Session>
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67 ]]></configfile>
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68 <configfile name="load_session">
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69 load igv_session.xml
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70 preference SAM.SHOW_SOFT_CLIPPED str($show_softclippped)
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71 </configfile>
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72 <configfile name="exit_session">
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73 exit
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74 </configfile>
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75 </configfiles>
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76 <inputs>
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77 <repeat name="inputfiles" min="1" title="Add tracks">
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78 <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file">
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79 <validator type="unspecified_build" />
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80 </param>
0
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81 <param name="label" type="text" label="Enter a label for this file. If no label is entered the history name will be used"/>
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82 <param name="section_height" type="integer" value="300" label="Height for this track"/>
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83 <param name="color_by_tag" type="text" value="CD" label="Enter a BAM/SAM tag that should detrmine the color of a read">
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84 <sanitizer invalid_char="">
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85 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
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86 </sanitizer>
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87 </param>
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88 </repeat>
9
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89 <param name="show_softclippped" type="boolean" label="Show softclipped bases?" truevalue="true" falsevalue="false" checked="true"/>
2
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90 <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/>
9
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91 <param name="width" label="Select the screenshot width" type="integer" min="800" value="1920"/>
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92 <param name="height" label="Select the screenshot height" type="integer" min="640" value="1080"/>
0
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93 </inputs>
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94 <outputs>
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95 <data name="igv_session_out" format="xml"/>
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96 <data name="screenshots_out" format="zip"/>
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97 </outputs>
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98 <help><![CDATA[
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99 TODO: Fill in help.
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100 ]]></help>
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101 </tool>