# HG changeset patch
# User mvdbeek
# Date 1501518029 14400
# Node ID fd2d19ae2648c17eae94c82e69ade01ffa933016
# Parent  46e42201f2e69660c063f47f56ace7a29b11f83a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit be45e3b0dec4ca1e8611abb2d84dd995e6d53751-dirty

diff -r 46e42201f2e6 -r fd2d19ae2648 igv_make_screenshots.xml
--- a/igv_make_screenshots.xml	Fri Jul 28 13:27:57 2017 -0400
+++ b/igv_make_screenshots.xml	Mon Jul 31 12:20:29 2017 -0400
@@ -1,9 +1,13 @@
 <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>
     <requirements>
         <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
         <requirement type="package" version="2.3.93">igv</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        #import re
         #if $genome_source.input_type_selector == 'history':
             ln -s '$genome_source.genome' genome.fa &&
         #else:
@@ -12,7 +16,7 @@
         samtools faidx genome.fa &&
         sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' &&
         #for $i, $inputsection in enumerate($inputfiles):
-            #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
+            @PATH@
             sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" '$igv_session' &&
             ln -fs '$inputsection.input' '$path' &&
             #if $inputsection.input.is_of_type('bam')
@@ -29,11 +33,12 @@
         cp screenshots.zip '$screenshots_out'
     ]]></command>
     <configfiles>
-        <configfile name="igv_session"><![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+        <configfile name="igv_session">#import re
+<![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8">
     <Resources>
         #for $i, $inputsection in enumerate($inputfiles):
-            #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
+            @PATH@
             #set $coverage_id="%s_coverage" % $path
         <Resource path="$path"/>
         #end for
@@ -41,7 +46,7 @@
     #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)
-            #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
+            @PATH
             <Panel height="$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">
@@ -59,7 +64,7 @@
         #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)
-                #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
+                @PATH@
                 <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="$path" name="$label" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>
              #end if
         #end for
@@ -75,6 +80,7 @@
         </configfile>
         <configfile name="igv_preferences">
 SAM.SHOW_SOFT_CLIPPED=$show_softclippped
+SAM.FILTER_SECONDARY_ALIGNMENTS=$filter_secondary
         </configfile>
     </configfiles>
     <inputs>
@@ -103,6 +109,7 @@
             </param>
         </repeat>
         <param name="show_softclippped" type="boolean" label="Show softclipped bases?" truevalue="true" falsevalue="false" checked="true"/>
+        <param name="filter_secondary" type="boolean" label="Filter out secondary reads" truevalue="true" falsevalue="false" checked="true"/>
         <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="800" value="1920"/>
         <param name="height" label="Select the screenshot height" type="integer" min="640" value="1080"/>
diff -r 46e42201f2e6 -r fd2d19ae2648 test-data/rover_corrected.bam.bai
Binary file test-data/rover_corrected.bam.bai has changed