# HG changeset patch
# User jackcurragh
# Date 1654601581 0
# Node ID 9445a308fb7ed62f3dbdd1b9d135127ca602c808
# Parent  0421e96d203a527f344fc515755ef64323edcc94
Uploaded

diff -r 0421e96d203a -r 9445a308fb7e samtools_sort_transcriptome/samtools_sort.xml
--- a/samtools_sort_transcriptome/samtools_sort.xml	Fri May 27 13:07:42 2022 +0000
+++ b/samtools_sort_transcriptome/samtools_sort.xml	Tue Jun 07 11:33:01 2022 +0000
@@ -7,6 +7,22 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
+        samtools sort
+            ###if str(compression):
+            ##    -l '$compression'
+            ###end if
+            $prim_key_cond.prim_key_select
+            #if $prim_key_cond.prim_key_select == '-t':
+                $prim_key_cond.tag
+                $prim_key_cond.sec_key_select
+            #end if
+            $minhash
+            -O bam
+            -T "\${TMPDIR:-.}"
+            '${input1}'
+             > '${output1}'
+    ]]>
+    <!-- <![CDATA[
         @ADDTHREADS@
 	@ADDMEMORY@
         samtools sort
@@ -25,7 +41,7 @@
             -T "\${TMPDIR:-.}"
             '${input1}'
              > '${output1}'
-    ]]></command>
+    ]]>--></command>
     <inputs>
         <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" />
         <conditional name="prim_key_cond">