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changeset 12:0149126ce6af draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:33:28 -0400
parents 797e773f1c3f
children cf4d627c5cc0
files samtools_sort.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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>