# HG changeset patch
# User iuc
# Date 1620310473 0
# Node ID 678ea22d643dc975b647fe18048c094cc9eb3a04
# Parent  b06c53665eb690dc89f6bd1971b74156822ebdc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"

diff -r b06c53665eb6 -r 678ea22d643d bamToBed.xml
--- a/bamToBed.xml	Tue Mar 23 20:21:30 2021 +0000
+++ b/bamToBed.xml	Thu May 06 14:14:33 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@">
+<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -8,8 +8,8 @@
     </expand>
     <expand macro="stdio" />
     <command><![CDATA[
-#if $input.extension == 'bam' and $option == "-bedpe":
-    samtools sort -n -T "\${TMPDIR:-.}" '${input}' ./input &&
+#if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
+    samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input &&
 #else
     ln -s '${input}' ./input.bam &&
 #end if
@@ -25,7 +25,7 @@
 > '${output}'
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="bam" label="Convert the following BAM file to BED"/>
+        <param name="input" type="data" format="unsorted.bam" label="Convert the following BAM file to BED"/>
         <param name="option" type="select" label="What type of BED output would you like">
             <option value="">Create a 6-column BED file</option>
             <option value="-bed12">Create a full, 12-column "blocked" BED file</option>