# HG changeset patch
# User iuc
# Date 1567726408 14400
# Node ID 0149126ce6af1683c78b2d620264a282b30a2e9a
# Parent  797e773f1c3ff283967cf212becef14e653fa5ea
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"

diff -r 797e773f1c3f -r 0149126ce6af samtools_sort.xml
--- a/samtools_sort.xml	Sun Jul 28 14:50:11 2019 -0400
+++ b/samtools_sort.xml	Thu Sep 05 19:33:28 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="samtools_sort" name="Samtools sort" version="2.0.2">
+<tool id="samtools_sort" name="Samtools sort" profile="18.01" version="2.0.3">
     <description>order of storing aligned sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -21,12 +21,12 @@
                 $prim_key_cond.sec_key_select
             #end if
             -O bam
-            -T sorttmp
+            -T "\${TMPDIR:-.}"
             '${input1}'
              > '${output1}'
     ]]></command>
     <inputs>
-        <param name="input1" type="data" format="sam,bam,cram" label="BAM File" />
+        <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" />
         <conditional name="prim_key_cond">
             <param name="prim_key_select" type="select" label="Primary sort key">
                 <option value="">coordinate</option>