# HG changeset patch
# User drosofff
# Date 1498686325 14400
# Node ID 2f4e22f2177d326b6e915e82c1891a019900b1e8
# Parent  411b6453b5d03c9dd32b99343ea08dfc6c78af0b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit cc96644a48fed1476e854fb7116b5f51c42f9f17

diff -r 411b6453b5d0 -r 2f4e22f2177d sRbowtie.xml
--- a/sRbowtie.xml	Tue Jun 27 04:49:57 2017 -0400
+++ b/sRbowtie.xml	Wed Jun 28 17:45:25 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="1.2">samtools</requirement>
+        <requirement type="package" version="1.2">bowtie</requirement>
+        <requirement type="package" version="1.4.1">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if str($refGenomeSource.genomeSource) == "history":
@@ -46,11 +46,11 @@
 
         ## run the bowtie alignement
         #if $output_format == "tabular":
-            bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' --suppress 6,7,8 '${extra_output}' local_index '${format}' '$input' > '$output'
+            bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' --suppress 6,7,8 '$extra_output' local_index '$format' '$input' > '$output'
         #elif $output_format == "sam":
-            bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' '${extra_output}' -S local_index '${format}' $input > $output
+            bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input > $output
         #elif $output_format == "bam":
-            bowtie -p \${GALAXY_SLOTS:-4} '${method_postfix}' '${extra_output}' -S local_index '${format}' $input |samtools view -bS - > $output
+            bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input | samtools sort -O bam -o '$output'
         #end if
         
         ]]></command>