# HG changeset patch
# User iuc
# Date 1499090939 14400
# Node ID 37a751a3bc79be8653ca82023913a99c7d525676
# Parent  4037db7d70d19a0ef86f18b9e0f7a91a24eb41f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit cadf726e05de4dfc4f2cf708674fcd2828e4c319

diff -r 4037db7d70d1 -r 37a751a3bc79 bam_to_scidx.xml
--- a/bam_to_scidx.xml	Fri Jan 13 10:23:13 2017 -0500
+++ b/bam_to_scidx.xml	Mon Jul 03 10:08:59 2017 -0400
@@ -3,21 +3,23 @@
     <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__/BAMtoscIDX.jar -b localbam.bam -i localbam.bam.bai -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null
-        ]]>
-    </command>
+    <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_bam}' localbam.bam &&
+ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
+java -jar '$__tool_directory__/BAMtoscIDX.jar'
+-b localbam.bam
+-i localbam.bam.bai
+-p $require_proper_mate_pairing
+-r $read
+#if str($min_insert_size):
+    -m $min_insert_size
+#end if
+#if str($max_insert_size):
+    -M $max_insert_size
+#end if
+-o '$output'
+1>/dev/null
+    ]]></command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="BAM file" />
         <param name="require_proper_mate_pairing" type="select" label="Require proper mate-pairing?" help="Required if filtering by insert size for single-end Reqd 1 (below)." >