diff pe_histogram.xml @ 2:9be99db0304a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3

--- a/pe_histogram.xml	Fri Jan 13 10:33:44 2017 -0500
+++ b/pe_histogram.xml	Tue Jul 11 14:36:59 2017 -0400
@@ -3,31 +3,22 @@
     <requirements>
         <requirement type="package" version="8.0.112">openjdk</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range=":-1" />
-        <exit_code range="1:" />
-        <!-- Check stderr in case the return code has not been set -->
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
-    <command>
-        <![CDATA[
-            ln -s "${input_bam}" "localbam.bam" &&
-            ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" &&
-            java -jar $__tool_directory__/PEHistogram.jar
-            -B "localbam.bam"
-            -I "localbam.bam.bai"
-            #if str($lower_limit) != '':
-                -l $lower_limit
-            #end if
-            #if str($upper_limit) != '':
-                -u $upper_limit
-            #end if
-            -p "$output1"
-            -t "$output2" 1>/dev/null
-        ]]>
-    </command>
+    <command detect_errors="aggressive"><![CDATA[
+ln -s '${input_bam}' localbam.bam &&
+ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
+java -jar '$__tool_directory__/PEHistogram.jar'
+-B localbam.bam
+-I localbam.bam.bai
+#if str($lower_limit):
+    -l $lower_limit
+#end if
+#if str($upper_limit):
+    -u $upper_limit
+#end if
+-p '$output1'
+-t '$output2'
+1>/dev/null
+    ]]></command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="BAM file" />
         <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/>