# HG changeset patch
# User drosofff
# Date 1499029828 14400
# Node ID 0d961f45e43e00219f04fee996eb21ed44539957
# Parent  7128df6248e5b362d9a24216b1b195683eced74e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b5e020763495240ddb730f757f0f30cafd208a6b-dirty

diff -r 7128df6248e5 -r 0d961f45e43e sRbowtie.xml
--- a/sRbowtie.xml	Sun Jul 02 16:41:35 2017 -0400
+++ b/sRbowtie.xml	Sun Jul 02 17:10:28 2017 -0400
@@ -1,8 +1,8 @@
 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2">
     <description>for FASTA small reads</description>
     <requirements>
-        <requirement type="package" version="1.1.2">bowtie</requirement>
-        <requirement type="package" version="1.3.1=py27_0">samtools</requirement>
+        <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if $refGenomeSource.genomeSource == "history":
@@ -50,7 +50,7 @@
         #elif $output_format == "sam":
             bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output'
         #elif $output_format == "bam":
-            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o $output
+            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output
         #end if
         ##### | samtools view -uS
         ]]></command>