Mercurial > repos > mvdbeek > igv_take_screenshots

annotate igv_make_screenshots.xml @ 32:9382c8499e73 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c6f25b122899a00695b5ca9e70d34e2c1d288236-dirty
author mvdbeek
date Sun, 20 Jan 2019 14:30:27 -0500
parents 474837e086cc
children 3f980046df62
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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__))
de2f2c28c498 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0437e9e56f0af2ccfb5f119b0f290109807ed9b0-dirty
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6 #set $galaxy_url = $__app__.config.galaxy_infrastructure_url
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7 #set $file_ext = $inputsection.input.extension
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8 #set $igv_ext = $file_ext if $file_ext != "gff3" else "gff"
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9 #set $element_identifier = $inputsection.input.element_identifier
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10 #set $display_link = "{galaxy_url}/display_application/{dataset_id}/igv_{igv_ext}/local_default/None/data/galaxy_{dataset_id}.{file_ext}".format(galaxy_url=galaxy_url, dataset_id=dataset_id, igv_ext=igv_ext, file_ext=file_ext, user_id=user_id)
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11 ]]></token>
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12 <token name="@PATH@"><![CDATA[
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13 #import re
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14 #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)
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15 ]]></token>
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16 </macros>
0
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17 <requirements>
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18 <!-- Conda can't give us a fully functioning xvfb at this time,
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19 need to use custom built container
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20 <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
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21 <requirement type="package" version="2.4.9">igv</requirement>
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22 <requirement type="package" version="1.6.6">xorg-libx11</requirement>
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23 <requirement type="package" version="1.17.4">xorg-x11-server-xvfb-cos6-x86_64</requirement>
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24 <requirement type="package" version="11.0.7">mesa-libgl-cos6-x86_64</requirement>
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25 <requirement type="package" version="2.0.94">libselinux-cos6-x86_64</requirement>
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26 <requirement type="package" version="1.0.2">openssl</requirement>
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27 <requirement type="package" version="1.9">samtools</requirement>
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28 <requirement type="package" version="8.30">coreutils</requirement>
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29 -->
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30 <container type="docker">mvdbeek/igv_make_screenshots:0.1.2</container>
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31 </requirements>
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32 <command detect_errors="exit_code"><![CDATA[
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33 #if $genome_source.input_type_selector == 'history':
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34 ln -s '$genome_source.genome' genome.fa &&
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35 #else:
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36 ln -s '$genome_source.genome.fields.path' genome.fa &&
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37 #end if
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38 samtools faidx genome.fa &&
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39 cp '$igv_session' igv_session.xml &&
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40 sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" igv_session.xml &&
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41 #for $i, $inputsection in enumerate($inputfiles):
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42 @PATH@
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43 ln -fs '$inputsection.input' '$path' &&
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44 sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" igv_session.xml &&
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45 #if $inputsection.input.is_of_type('bam')
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46 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
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47 #end if
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48 #end for
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49 cat '$load_session' > load_session.txt &&
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50 echo snapshotDirectory "\$PWD" >> load_session.txt &&
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51 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
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52 cp '$igv_session_remote' '$igv_session_out'
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53 #if not $skip_screenshots:
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54 && xvfb-run --server-args="-screen 0 ${width}x${height}x24" igv -g genome.fa -o '$igv_preferences' --batch igv_script.txt &&
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55 mkdir screenshots && mv *.png screenshots
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56 #end if
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57 ]]></command>
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58 <configfiles>
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59 <configfile name="igv_session"><![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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60 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8">
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61 <Resources>
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62 #for $i, $inputsection in enumerate($inputfiles):
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63 @PATH@
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64 #set $coverage_id="%s_coverage" % $path
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65 <Resource path="$path"/>
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66 #end for
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67 </Resources>
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68 #for $i, $inputsection in enumerate($inputfiles):
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69 #if $inputsection.input.is_of_type('bam')
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70 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
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71 @PATH@
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72 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
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73 ## First track is the coverage
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74 <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
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75 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
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76 </Track>
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77 ## Second track is the actual BAM alignment file
2
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78 <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" sortable="true" visible="true">
0
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79 <RenderOptions colorByTag="$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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80 </Track>
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81 </Panel>
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82 #end if
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83 #end for
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84 <Panel height="186" name="FeaturePanel" width="$width">
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85 <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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86 #for $i, $inputsection in enumerate($inputfiles):
0
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87 #if not $inputsection.input.is_of_type('bam')
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88 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
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89 @PATH@
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90 <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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91 #end if
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92 #end for
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93 </Panel>
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94 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
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95 </Session>
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96 ]]></configfile>
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97 <configfile name="igv_session_remote"><![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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98 <Session genome="dm6" hasGeneTrack="true" hasSequenceTrack="true" version="8">
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99 <Resources>#for $i, $inputsection in enumerate($inputfiles):@DISPLAY_LINK@<Resource path="$display_link"/>#end for
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100 </Resources>
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101 #for $i, $inputsection in enumerate($inputfiles):
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102 #if $inputsection.input.is_of_type('bam')
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103 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
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104 @DISPLAY_LINK@
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105 #set $coverage_id="%s_coverage" % $display_link
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106 <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
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107 ## First track is the coverage
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108 <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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109 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
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110 </Track>
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111 ## Second track is the actual BAM alignment file
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112 <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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113 <RenderOptions colorByTag="$inputsection.color_by_tag" colorOption="TAG" flagUnmappedPairs="false" groupByOption="NONE" groupByTag="BR" linkByTag="READNAME" linkedReads="false" maxInsertSize="1000" minInsertSize="50" quickConsensusMode="false" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag="" viewPairs="false"/>
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114 </Track>
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115 </Panel>
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116 #end if
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117 #end for
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118 <Panel height="186" name="FeaturePanel" width="$width">
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119 <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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120 #for $i, $inputsection in enumerate($inputfiles):
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121 #if not $inputsection.input.is_of_type('bam')
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122 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
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123 @DISPLAY_LINK@
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124 <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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125 #end if
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126 #end for
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127 </Panel>
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128 <PanelLayout dividerFractions="0.004995836802664446,0.12905911740216486,0.2681099084096586,0.5512073272273106,0.8409658617818485"/>
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129 </Session>
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130 ]]></configfile>
0
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131 <configfile name="load_session">
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132 load igv_session.xml
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133 </configfile>
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134 <configfile name="exit_session">
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135 exit
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136 </configfile>
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137 <configfile name="igv_preferences">
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138 SAM.SHOW_SOFT_CLIPPED=$show_softclippped
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139 </configfile>
0
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140 </configfiles>
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141 <inputs>
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142 <conditional name="genome_source">
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143 <param name="input_type_selector" type="select" label="Choose the genome source">
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144 <option value="cached" selected="True">Built-in references</option>
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145 <option value="history">Select a fasta file from your history</option>
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146 </param>
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147 <when value="cached">
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148 <param name="genome" type="select" label="Select a genome">
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149 <options from_data_table="all_fasta" />
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150 </param>
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151 </when>
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152 <when value="history">
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153 <param name="genome" type="data" format="fasta" label="Select a fasta file as reference genome"/>
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154 </when>
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155 </conditional>
0
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156 <repeat name="inputfiles" min="1" title="Add tracks">
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157 <param name="input" type="data" format="bam,gff,gff3,gtf,bed,vcf" label="Choose an input file"/>
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158 <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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159 <param name="section_height" type="integer" value="300" label="Height for this track"/>
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160 <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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161 <sanitizer invalid_char="">
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162 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
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163 </sanitizer>
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164 </param>
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165 </repeat>
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166 <param name="skip_screenshots" type="boolean" label="Skip taking screenshots? Only produces session files."/>
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167 <param name="show_softclippped" type="boolean" label="Show softclipped bases?" truevalue="true" falsevalue="false" checked="true"/>
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168 <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/>
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169 <param name="width" label="Select the screenshot width" type="integer" min="800" value="1920"/>
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170 <param name="height" label="Select the screenshot height" type="integer" min="640" value="1080"/>
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171 </inputs>
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172 <outputs>
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173 <data name="igv_session_out" format="xml" label="IGV session for ${on_string}"/>
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174 <collection name="screenshots_out" type="list" label="IGV screenshots for ${on_string}">
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175 <filter>skip_screenshots == False</filter>
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176 <discover_datasets pattern="__name_and_ext__" directory="screenshots" />
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177 </collection>
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178 </outputs>
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179 <tests>
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180 <test>
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181 <param name="genome_source|input_type_selector" value="history"/>
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182 <param name="genome_source|genome" value="rover_reference.fa"/>
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183 <param name="script_file" value="complete_batchscript.txt"/>
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184 <repeat name="inputfiles">
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185 <param name="input" value="rover_corrected.bam"/>
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186 </repeat>
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187 <output name="igv_session_out" file="igv_session.xml" lines_diff="6"/>
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188 <output_collection name="screenshots_out" type="list" count="1"/>
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189 </test>
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190 </tests>
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191 <help><![CDATA[
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192 This tool can automate taking screenshots using IGV.
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193 It takes as input a reference genome, an IGV script file (bedtools igv can produce such a file)
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194 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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195 ]]></help>
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196 <citations>
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197 <citation type="doi">10.1093/bib/bbs017</citation>
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198 </citations>
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199 </tool>