# HG changeset patch
# User drosofff
# Date 1478708551 18000
# Node ID a0bde9b84ca6f5ea74eb6eae6fdb1b134a4518e9
# Parent  88cdd6118bfec3d9ddc2c35a21805da6903e1ce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07

diff -r 88cdd6118bfe -r a0bde9b84ca6 sRbowtie.py
--- a/sRbowtie.py	Mon Sep 28 16:47:11 2015 -0400
+++ b/sRbowtie.py	Wed Nov 09 11:22:31 2016 -0500
@@ -181,7 +181,7 @@
     else:
         tmp_dir, index_path = "dummy/dymmy", args.index_source
     command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format,
-                                      args.aligned, args.unaligned, args.input_format, args.input, 
+                                      args.aligned, args.unaligned, args.input_format, args.input,
                                       index_path, args.output, args.num_threads)
     bowtie_alignment(command_line, flyPreIndexed=tmp_dir)
     F.close()
diff -r 88cdd6118bfe -r a0bde9b84ca6 sRbowtie.xml
--- a/sRbowtie.xml	Mon Sep 28 16:47:11 2015 -0400
+++ b/sRbowtie.xml	Wed Nov 09 11:22:31 2016 -0500
@@ -1,27 +1,29 @@
-<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.2">
+<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.2.1">
     <description>for FASTA small reads</description>
     <requirements>
-        <requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="1.1.2">bowtie</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
-    <command interpreter="python"> sRbowtie.py --input $input
-                                             --input-format $input.extension
-                                             --method $method
-                                             --v-mismatches $v_mismatches
-                                             --output-format $output_format
-                                             --output $output
-                                             --index-from $refGenomeSource.genomeSource
-                                             ## the very source of the index (indexed or fasta file)
-                                             --index-source
-                                             #if $refGenomeSource.genomeSource == "history":
-                                                 $refGenomeSource.ownFile
-                                             #else:
-                                                 $refGenomeSource.index.fields.path
-                                             #end if
-                                             --aligned $aligned
-                                             --unaligned $unaligned
-                                             --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
-  </command>
+    <command><![CDATA[
+        python '$__tool_directory__'/sRbowtie.py
+        --input '$input'
+        --input-format '$input.extension'
+        --method '$method'
+        --v-mismatches $v_mismatches
+        --output-format $output_format
+        --output '$output'
+        --index-from '$refGenomeSource.genomeSource'
+        ## the very source of the index (indexed or fasta file)
+        --index-source
+        #if $refGenomeSource.genomeSource == "history":
+            '$refGenomeSource.ownFile'
+        #else:
+            '$refGenomeSource.index.fields.path'
+        #end if
+        --aligned '$aligned'
+        --unaligned '$unaligned'
+        --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
+        ]]></command>
     <inputs>
         <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
         <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
diff -r 88cdd6118bfe -r a0bde9b84ca6 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Sep 28 16:47:11 2015 -0400
+++ b/tool_dependencies.xml	Wed Nov 09 11:22:31 2016 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="bowtie" version="0.12.7">
-         <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="bowtie" version="1.1.2">
+         <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="1.2">
-         <repository changeset_revision="9cd278d52bb6" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+         <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>