Mercurial > repos > mvdbeek > igv_take_screenshots

changeset 20:1f8609ae3941 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit be45e3b0dec4ca1e8611abb2d84dd995e6d53751-dirty
author mvdbeek
date Mon, 31 Jul 2017 12:45:19 -0400
parents fd2d19ae2648
children de2f2c28c498
files igv_make_screenshots.xml
diffstat 1 files changed, 5 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/igv_make_screenshots.xml	Mon Jul 31 12:20:29 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jul 31 12:45:19 2017 -0400
@@ -1,7 +1,4 @@
-<tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.0">
-    <macros>
-        <token name="@PATH@"><![CDATA[#set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)]]></token>
-    </macros>
+<tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.1">
     <requirements>
         <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
         <requirement type="package" version="2.3.93">igv</requirement>
@@ -16,7 +13,7 @@
         samtools faidx genome.fa &&
         sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' &&
         #for $i, $inputsection in enumerate($inputfiles):
-            @PATH@
+            #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)
             sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" '$igv_session' &&
             ln -fs '$inputsection.input' '$path' &&
             #if $inputsection.input.is_of_type('bam')
@@ -38,7 +35,7 @@
 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8">
     <Resources>
         #for $i, $inputsection in enumerate($inputfiles):
-            @PATH@
+            #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)
             #set $coverage_id="%s_coverage" % $path
         <Resource path="$path"/>
         #end for
@@ -46,7 +43,7 @@
     #for $i, $inputsection in enumerate($inputfiles):
         #if $inputsection.input.is_of_type('bam')
             #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
-            @PATH
+            #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $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">
@@ -64,7 +61,7 @@
         #for $i, $inputsection in enumerate($inputfiles):
             #if not $inputsection.input.is_of_type('bam')
                 #set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
-                @PATH@
+                #set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $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