Mercurial > repos > mvdbeek > igv_take_screenshots

annotate igv_make_screenshots.xml @ 25:c96924da37af draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0437e9e56f0af2ccfb5f119b0f290109807ed9b0-dirty
author mvdbeek
date Fri, 15 Jun 2018 12:56:58 -0400
parents 2b4c4b610be6
children 6f98222928ee
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mvdbeek
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1 <tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.2">
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2 <macros>
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3 <token name="@DISPLAY_LINK@"><![CDATA[
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mvdbeek
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4 #set $dataset_id = str($__app__.security.encode_id($inputsection.input.dataset.id))
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mvdbeek
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5 #set $user_id = str($__app__.security.encode_id($__user_id__))
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6 #set $galaxy_url = $__app__.config.galaxy_infrastructure_url
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7 #set $ext = $inputsection.input.extension
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8 #set $element_identifier = $inputsection.input.element_identifier
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9 #set $display_link = "{galaxy_url}/display_application/{dataset_id}/igv_{ext}/local_default/None/data/galaxy_{dataset_id}.{ext}".format(galaxy_url=galaxy_url, dataset_id=dataset_id, ext=ext, user_id=user_id)
21
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10 ]]></token>
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11 <token name="@PATH@"><![CDATA[#set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)]]></token>
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12 </macros>
0
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13 <requirements>
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14 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
21
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15 <!-- TODO: uncomment when igv in conda
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16 <requirement type="package" version="2.3.93">igv</requirement>
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17 -->
0
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18 </requirements>
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19 <command detect_errors="exit_code"><![CDATA[
21
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20 #import re
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21 #if $genome_source.input_type_selector == 'history':
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22 ln -s '$genome_source.genome' genome.fa &&
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23 #else:
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24 ln -s '$genome_source.genome.fields.path' genome.fa &&
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25 #end if
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26 samtools faidx genome.fa &&
de2f2c28c498 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0437e9e56f0af2ccfb5f119b0f290109807ed9b0-dirty
mvdbeek
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27 sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' &&
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28 #for $i, $inputsection in enumerate($inputfiles):
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29 @PATH@
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30 ln -fs '$inputsection.input' '$path' &&
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31 #if $inputsection.input.is_of_type('bam')
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32 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
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33 #end if
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34 #end for
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35 ln -fs $igv_session igv_session.xml &&
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36 cat '$load_session' > load_session.txt &&
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37 echo snapshotDirectory "\$PWD" >> load_session.txt &&
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38 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
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39 cp '$igv_session_remote' '$igv_session_out'
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40 #if not $skip_screenshots:
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41 && python $__tool_directory__/xvfb_igv.py igv_script.txt '$igv_preferences' $width,$height &&
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42 zip screenshots.zip *.png &&
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43 cp screenshots.zip '$screenshots_out'
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44 #end if
0
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45 ]]></command>
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46 <configfiles>
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47 <configfile name="igv_session">
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48 <![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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49 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8">
0
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50 <Resources>
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51 #for $i, $inputsection in enumerate($inputfiles):
21
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52 @PATH@
2
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53 #set $coverage_id="%s_coverage" % $path
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54 <Resource path="$path"/>
0
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55 #end for
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56 </Resources>
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57 #for $i, $inputsection in enumerate($inputfiles):
0
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58 #if $inputsection.input.is_of_type('bam')
2
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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 @PATH
0
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61 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
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62 ## First track is the coverage
2
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63 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
0
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64 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
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65 </Track>
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66 ## Second track is the actual BAM alignment file
2
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67 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" sortable="true" visible="true">
0
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68 <RenderOptions colorByTag="$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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69 </Track>
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70 </Panel>
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71 #end if
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72 #end for
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73 <Panel height="186" name="FeaturePanel" width="$width">
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74 <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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75 #for $i, $inputsection in enumerate($inputfiles):
0
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76 #if not $inputsection.input.is_of_type('bam')
2
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77 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
21
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78 @PATH@
2
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79 <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"/>
0
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80 #end if
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81 #end for
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82 </Panel>
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83 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
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84 </Session>
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85 ]]></configfile>
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86 <configfile name="igv_session_remote">
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87 <![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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88 <Session genome="dm6" hasGeneTrack="true" hasSequenceTrack="true" version="8">
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89 <Resources>#for $i, $inputsection in enumerate($inputfiles):@DISPLAY_LINK@<Resource path="$display_link"/>#end for
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90 </Resources>
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91 #for $i, $inputsection in enumerate($inputfiles):
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92 #if $inputsection.input.is_of_type('bam')
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93 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
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94 @DISPLAY_LINK@
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95 #set $coverage_id="%s_coverage" % $display_link
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96 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
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97 ## First track is the coverage
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98 <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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99 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
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100 </Track>
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101 ## Second track is the actual BAM alignment file
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102 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="$display_link" name="$label" sortable="true" visible="true">
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103 <RenderOptions colorByTag="$inputsection.color_by_tag" colorOption="TAG" flagUnmappedPairs="false" groupByOption="NONE" groupByTag="BR" linkByTag="READNAME" linkedReads="false" maxInsertSize="1000" minInsertSize="50" quickConsensusMode="false" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag="" viewPairs="false"/>
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104 </Track>
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105 </Panel>
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106 #end if
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107 #end for
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108 <Panel height="186" name="FeaturePanel" width="$width">
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109 <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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110 #for $i, $inputsection in enumerate($inputfiles):
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111 #if not $inputsection.input.is_of_type('bam')
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112 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
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113 @DISPLAY_LINK@
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114 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$display_link" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
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115 #end if
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116 #end for
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117 </Panel>
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118 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
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119 </Session>
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120 ]]></configfile>
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121 <configfile name="load_session">
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122 load igv_session.xml
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123 </configfile>
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124 <configfile name="exit_session">
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125 exit
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126 </configfile>
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127 <configfile name="igv_preferences">
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128 SAM.SHOW_SOFT_CLIPPED=$show_softclippped
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129 </configfile>
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130 </configfiles>
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131 <inputs>
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132 <conditional name="genome_source">
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133 <param name="input_type_selector" type="select" label="Choose the genome source">
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134 <option value="cached" selected="True">Built-in references</option>
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135 <option value="history">Select a fasta file from your history</option>
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136 </param>
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137 <when value="cached">
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138 <param name="genome" type="select" label="Select a genome">
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139 <options from_data_table="all_fasta" />
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140 </param>
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141 </when>
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142 <when value="history">
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143 <param name="genome" type="data" format="fasta" label="Select a fasta file as reference genome"/>
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144 </when>
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145 </conditional>
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146 <repeat name="inputfiles" min="1" title="Add tracks">
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147 <param name="input" type="data" format="bam,gff,gff3,gtf,bed,vcf" label="Choose an input file"/>
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148 <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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149 <param name="section_height" type="integer" value="300" label="Height for this track"/>
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150 <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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151 <sanitizer invalid_char="">
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152 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
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153 </sanitizer>
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154 </param>
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155 </repeat>
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156 <param name="skip_screenshots" type="boolean" label="Skip taking screenshots? Only produces session files."/>
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157 <param name="show_softclippped" type="boolean" label="Show softclipped bases?" truevalue="true" falsevalue="false" checked="true"/>
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158 <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/>
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159 <param name="width" label="Select the screenshot width" type="integer" min="800" value="1920"/>
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160 <param name="height" label="Select the screenshot height" type="integer" min="640" value="1080"/>
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161 </inputs>
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162 <outputs>
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163 <data name="igv_session_out" format="xml"/>
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164 <data name="screenshots_out" format="zip">
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165 <filter>skip_screenshots == False</filter>
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166 </data>
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167 </outputs>
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168 <tests>
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169 <test>
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170 <param name="genome_source|input_type_selector" value="history"/>
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171 <param name="genome_source|genome" value="rover_reference.fa"/>
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172 <repeat name="inputfiles">
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173 <param name="input" value="rover_corrected.bam"/>
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174 </repeat>
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175 <output name="igv_session_out" file="igv_session.xml" lines_diff="6"/>
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176 </test>
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177 </tests>
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178 <help><![CDATA[
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179 This tool can automate taking screenshots using IGV.
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180 It takes as input a reference genome, an IGV script file (bedtools igv can produce such a file)
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181 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.
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182 ]]></help>
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183 <citations>
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184 <citation type="doi">10.1093/bib/bbs017</citation>
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185 </citations>
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186 </tool>