# HG changeset patch
# User iuc
# Date 1403513900 14400
# Node ID 38ea74bd4054601361c2f8089ee83baa371653f6
# Parent  f627c4b93c551b69f564a99847789f9ac3b9fc97
Uploaded

diff -r f627c4b93c55 -r 38ea74bd4054 samtools_sort.xml
--- a/samtools_sort.xml	Fri Jun 20 14:37:57 2014 -0400
+++ b/samtools_sort.xml	Mon Jun 23 04:58:20 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="samtools_sort" name="sort" version="1.0.1">
+<tool id="samtools_sort" name="sort" version="1.0.2">
     <requirements>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
@@ -6,14 +6,16 @@
     <command>
         samtools sort
             $sort_mode
-            "${input1}" "${output1}"
+            "${input1}" foo
             2&gt;&amp;1 || echo "Error running samtools sort." &gt;&amp;2
+            ;
+            mv foo.bam "${output1}"
     </command>
     <inputs>
         <param name="input1" type="data" format="bam" label="BAM File" />
         <param name="sort_mode" type="select" label="Sort by ">
-            <option value="" selected="True">chromosomal coordinates </option>
-            <option value="-n">read names rather than by</option>
+            <option value="" selected="True">Chromosomal coordinates</option>
+            <option value="-n">Read names</option>
         </param>
     </inputs>
     <outputs>
@@ -22,7 +24,7 @@
     <tests>
         <test>
             <param name="input1" value="1.bam" ftype="bam" />
-            <output name="output1" file="1.bam" ftype="bam" sort="True"/>
+            <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
         </test>
     </tests>
     <help>
diff -r f627c4b93c55 -r 38ea74bd4054 test-data/1_sort.bam
Binary file test-data/1_sort.bam has changed