Mercurial > repos > mvdbeek > igv_take_screenshots

changeset 3:f44435b6ad19 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 08:46:22 -0400
parents 18e36ab5e669
children a4877f60773a
files igv_make_screenshots.xml
diffstat 1 files changed, 5 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/igv_make_screenshots.xml	Mon Jul 03 08:05:41 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jul 03 08:46:22 2017 -0400
@@ -5,6 +5,8 @@
     <command detect_errors="exit_code"><![CDATA[
         #for $inputsection in $inputfiles
             #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
+            #set $abspath=os.path.abspath($path)
+            sed -i.bak -e 's|$path|$abspath|g' '$igv_session' &&
             ln -fs $inputsection.input $path &&
             #if $inputsection.input.is_of_type('bam')
                 ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
@@ -23,9 +25,8 @@
 <?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 $path=os.path.abspath("%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension))
+            #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
             #set $coverage_id="%s_coverage" % $path
         <Resource path="$path"/>
         #end for
@@ -33,7 +34,7 @@
     #for $inputsection in $inputfiles
         #if $inputsection.input.is_of_type('bam')
             #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))
+            #set $path="%s.%s" % ($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="$coverage_id" name="$label Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
@@ -54,7 +55,7 @@
         #for $inputsection in $inputfiles
             #if not $inputsection.input.is_of_type('bam')
                 #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))
+                #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"/>
              #end if
         #end for