Mercurial > repos > mvdbeek > igv_take_screenshots

changeset 2:18e36ab5e669 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 08:05:41 -0400
parents 8b80357d8ab1
children f44435b6ad19
files igv_make_screenshots.xml test-data/rover_dont_split.bam.bai
diffstat 2 files changed, 15 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/igv_make_screenshots.xml	Mon Jun 26 10:17:15 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jul 03 08:05:41 2017 -0400
@@ -23,22 +23,24 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <Session genome="${genome}" hasGeneTrack="true" hasSequenceTrack="true" version="8">
     <Resources>
+        #import os
         #for $inputsection in $inputfiles
-            #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
-        <Resource name="$inputsection.input.element_identifier" path="$path"/>
+            #set $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension))
+            #set $coverage_id="%s_coverage" % $path
+        <Resource path="$path"/>
         #end for
     </Resources>
     #for $inputsection in $inputfiles
         #if $inputsection.input.is_of_type('bam')
-            #set $label=$inputsection.label if not $inputsection.label == '' else $inputsection.input.element_identifier
-            #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
+            #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
+            #set $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension))
             <Panel height="$inputsection.section_height" name="Panel${label}" width="$width">
             ## First track is the coverage
-            <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">
+            <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">
                 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
             </Track>
             ## Second track is the actual BAM alignment file
-            <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="label" sortable="true" visible="true">
+            <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" sortable="true" visible="true">
                 <RenderOptions colorByTag="$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"/>
             </Track>
             </Panel>
@@ -51,9 +53,9 @@
         </Track>
         #for $inputsection in $inputfiles
             #if not $inputsection.input.is_of_type('bam')
-                #set $label=$inputsection.label if not $inputsection.label == '' else $inputsection.input.element_identifier
-                #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
-                <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="${path}" name="${label}" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
+                #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
+                #set $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension))
+                <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
              #end if
         #end for
     </Panel>
@@ -69,7 +71,9 @@
     </configfiles>
     <inputs>
         <repeat name="inputfiles" min="1" title="Add tracks">
-            <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file"/>
+            <param name="input" type="data" format="bam,gff,gtf,bed,vcf" label="Choose an input file">
+                    <validator type="unspecified_build" />
+            </param>
             <param name="label" type="text" label="Enter a label for this file. If no label is entered the history name will be used"/>
             <param name="section_height" type="integer" value="300" label="Height for this track"/>
             <param name="color_by_tag" type="text" value="CD" label="Enter a BAM/SAM tag that should detrmine the color of a read">
@@ -78,7 +82,7 @@
                 </sanitizer>
             </param>
         </repeat>
-        <param name="script_file" type="data" format="text" label="Select a IGV script with regions for which to take screenshots"/>
+        <param name="script_file" type="data" format="txt" label="Select a IGV script with regions for which to take screenshots"/>
         <param name="width" label="Select the screenshot width" type="integer" min="640" value="1080"/>
         <param name="height" label="Select the screenshot height" type="integer" min="800" value="1920"/>
     </inputs>
Binary file test-data/rover_dont_split.bam.bai has changed