# HG changeset patch
# User mvdbeek
# Date 1529085678 14400
# Node ID 9d6b4d2ca1878894cc4a462e03ce82d92155d978
# Parent  dd61761307ca1ea7016adc0eae91be830452777a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0437e9e56f0af2ccfb5f119b0f290109807ed9b0-dirty

diff -r dd61761307ca -r 9d6b4d2ca187 igv_make_screenshots.xml
--- a/igv_make_screenshots.xml	Fri Jun 15 13:33:51 2018 -0400
+++ b/igv_make_screenshots.xml	Fri Jun 15 14:01:18 2018 -0400
@@ -9,7 +9,10 @@
 #set $element_identifier = $inputsection.input.element_identifier
 #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)
 ]]></token>
-        <token name="@PATH@"><![CDATA[#set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)]]></token>
+        <token name="@PATH@"><![CDATA[
+#import re
+#set $path="%s.%s.%s" % ($i, re.sub('[^\w\-_]', '_', $inputsection.input.element_identifier), $inputsection.input.extension)
+]]></token>
     </macros>
     <requirements>
         <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
@@ -57,7 +60,7 @@
     #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
+            @PATH@
             <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">