changeset 2:6432735cdb22 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce

--- a/tag_pileup_frequency.xml	Fri Jan 13 10:35:07 2017 -0500
+++ b/tag_pileup_frequency.xml	Fri Jun 16 14:13:32 2017 -0400
@@ -3,31 +3,29 @@
     <requirements>
         <requirement type="package" version="8.0.112">openjdk</requirement>
     </requirements>
-    <command>
-        <![CDATA[
-            mkdir -p output &&
-            ln -f -s "${input1.metadata.bam_index}" "${input1}.bai" &&
-            java -jar $__tool_directory__/TagPileup.jar
-            -b "$input1"
-            -i "${input1}.bai"
-            -c "$input2"
-            -s $tag_shift
-            -n $bin_size
-            -e $tags_equal
-            -r $reads
-            -p $proper_pe
-            -a $combine_strands
-            -t "\${GALAXY_SLOTS:-4}"
-            -w $composite_smoothing_window
-            -m "true"
-            -x "$output1"
-            -h $output_heatmap
-            #if str($output_heatmap) == "true":
-                -o output
-            #end if
-            1>/dev/null
-        ]]>
-    </command>
+    <command detect_errors="exit_code"><![CDATA[
+mkdir -p output &&
+ln -f -s '${input1.metadata.bam_index}' '${input1}.bai' &&
+java -jar '$__tool_directory__/TagPileup.jar'
+-b '$input1'
+-i '${input1}.bai'
+-c '$input2'
+-s $tag_shift
+-n $bin_size
+-e $tags_equal
+-r $reads
+-p $proper_pe
+-a $combine_strands
+-t "\${GALAXY_SLOTS:-4}"
+-w $composite_smoothing_window
+-m true
+-x '$output1'
+-h $output_heatmap
+#if str($output_heatmap) == "true":
+    -o output
+#end if
+1>/dev/null
+    ]]></command>
     <inputs>
         <param name="input1" type="data" format="bam" label="BAM file" />
         <param name="input2" type="data" format="bed" label="Bed file" />