# HG changeset patch
# User drosofff
# Date 1478708444 18000
# Node ID 615d2550977f6ad67c4bc517a0025f8651a48f7f
# Parent  68b71bd388eb8acbab638dd8cce31397fd5e77dc
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07

diff -r 68b71bd388eb -r 615d2550977f sRbowtie.py
--- a/sRbowtie.py	Sun Sep 18 12:54:55 2016 -0400
+++ b/sRbowtie.py	Wed Nov 09 11:20:44 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 68b71bd388eb -r 615d2550977f sRbowtie.xml
--- a/sRbowtie.xml	Sun Sep 18 12:54:55 2016 -0400
+++ b/sRbowtie.xml	Wed Nov 09 11:20:44 2016 -0500
@@ -4,24 +4,26 @@
         <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">