# HG changeset patch
# User scisjnu123
# Date 1569588946 14400
# Node ID 765d954df8bfdc0702c6fdb4852f6dff3eafa11a
# Parent  d6b1131dd9f20bdfe17a0ec0120222d4aa2a67be
Uploaded

diff -r d6b1131dd9f2 -r 765d954df8bf samtools_sort/samtools_sort.xml
--- a/samtools_sort/samtools_sort.xml	Fri Sep 27 08:42:59 2019 -0400
+++ b/samtools_sort/samtools_sort.xml	Fri Sep 27 08:55:46 2019 -0400
@@ -6,7 +6,7 @@
   <expand macro="requirements"></expand>
     <expand macro="stdio"></expand>
     <expand macro="version_command"></expand>
-    <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
+    <command>samtools sort "${input1}" "${output1}"</command>
     <inputs>
         <param name="input1" type="data" format="bam" label="BAM File" />
         <param name="sort_mode" type="select" label="Sort by ">
@@ -17,24 +17,6 @@
     <outputs>
         <data name="output1" format="bam" />
     </outputs>
-    <tests>
-        <test>
-            <param name="input1" value="1.bam" ftype="bam" />
-            <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
-        </test>
-        <test>
-            <param name="input1" value="1.bam" ftype="bam" />
-            <param name="sort_mode" value="-n"/>
-            <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/>
-        </test>
-    </tests>
-    <help>
-
-**What it does**
-
-This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
-
-
-    </help>
+   
     <expand macro="citations"></expand>
 </tool>