--- a/sRbowtie.xml	Mon Jun 26 06:17:32 2017 -0400
+++ b/sRbowtie.xml	Mon Jun 26 12:06:12 2017 -0400
@@ -1,28 +1,56 @@
-<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.2.2">
+<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>
     </requirements>
-    <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
+    <command detect_errors="exit_code"><![CDATA[
         #if $refGenomeSource.genomeSource == "history":
-            '$refGenomeSource.ownFile'
+            bowtie-build -f '$refGenomeSource.ownFile' local_index &&
         #else:
-            '$refGenomeSource.index.fields.path'
+            ln -s local_index '$refGenomeSource.index.fields.path' &&
+        #end if
+        #if $input.extension == "fasta":
+            #set format = "-f"
+        #elif $input.extension == "fastq":
+            #set format = "-q"
         #end if
-        --aligned '$aligned'
-        --unaligned '$unaligned'
-        --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
+
+        ## set the method_prefix
+        #if $method == "RNA":
+            #set method_prefix = "-v %s -M 1 --best --strata --norc" % (str($v_mismatches))
+        #elif $method == "unique":
+            #set method_prefix = "-v %s -m 1" % (str($v_mismatches))
+        #elif $method == "multiple":
+            #set method_prefix = "-v %s -M 1 --best --strata" % (str($v_mismatches))
+        #elif $method == "k_option":
+            #set method_prefix = "-v %s -k 1 --best" % (str($v_mismatches))
+        #elif $method == "n_option":
+            #set method_prefix = "-n %s -M 1 --best" % (str($v_mismatches))
+        #elif $method == "a_option":
+            #set method_prefix = "-v %s -a --best" % (str($v_mismatches))
+        #end if
+ 
+        ## set the extra_output
+        #if $additional_fasta == "No":
+            #set extra_output = ""
+        #elif $additional_fasta == "al":
+            #set extra_output = " --un %s" % str(unaligned)
+        #else:
+            #set extra_output = " --al %s --un %s" % (str($aligned), str(unaligned))
+        #end if
+       
+        #set $method_postfix = "$method_prefix" + "$extra_output"
+
+        ## run the bowtie alignement
+        #if $output_format == "tabular":
+            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix  --suppress 6,7,8 "local_index" $format $input > $output
+        #elif $output_format == "sam":
+            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input > $output
+        #elif $output_format == "bam":
+            bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input |samtools view -bS - > $output
+        #end if
+        
         ]]></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" />