--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtieParser.xml	Wed May 27 17:19:15 2015 -0400
@@ -0,0 +1,87 @@
+<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1">
+  <description></description>
+  <requirements>
+	<requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="0.7.7">pysam</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="0.14">scipy</requirement>
+ </requirements>
+<command interpreter="python">
+        sRbowtieParser.py 
+	          #if $refGenomeSource.genomeSource == "history":
+                    --IndexSource $refGenomeSource.ownFile
+         	    --ExtractDirective fastaSource
+          	  #else:
+		    #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
+            	    --IndexSource $reference
+            	    --ExtractDirective bowtieIndex
+          	  #end if
+		  --output $output
+		  --polarity $polarity
+                  --alignmentSource
+		  #for $i in $refGenomeSource.input_list
+    		    $i
+		  #end for
+                  --alignmentFormat
+                  #for $i in $refGenomeSource.input_list
+                    $i.ext
+                  #end for
+                  --alignmentLabel          
+                  #for $i in $refGenomeSource.input_list
+                    "$i.name"
+                  #end for
+
+</command>
+  <inputs>
+       <conditional name="refGenomeSource">
+           <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+               <option value="indexed">Use a built-in index</option>
+               <option value="history">Use one from the history</option>
+           </param>
+           <when value="indexed">
+               <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true">
+                  <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
+               </param>
+           </when>
+           <when value="history">
+                <param name="ownFile" type="data" format="fasta"  label="Select the fasta reference" />
+	        <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/>
+           </when>
+       </conditional>  <!-- refGenomeSource -->
+       <param name="polarity" type="select" label="how to count sense and antisense reads">
+         <option value="both">count both sense and antisense reads</option>
+         <option value="forward">count only sense reads</option>
+         <option value="reverse">count only antisense reads</option>
+       </param>
+   </inputs>
+   <outputs>
+   <data format="tabular" name="output" label="Read Count  Lists"/>
+   </outputs>
+  <help>
+
+**What it does**
+
+Parses read counts from one or several sRBowtie alignments (in tabular, Sam or Bam format).
+Here a bowtie match done against an index composed of a set of items is parsed and expressed as a hit list of the corresponding items
+
+Sense, antisense or both sense and antisense alignments can be counted
+
+The library labels are infered from the input dataset names in the galaxy history.
+
+**It is thus essential that input datasets are appropriately renamed**
+
+**it is preferable that you do not put any space in this input dataset names. You may edit these names in the history**
+
+  </help>
+  <tests>
+    <test>
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" value ="dme-mir-v20" ftype="fasta" />
+      <param name="input_list" value="matchedSample_1,matchedSample_2" ftype="tabular" />
+      <param name="polarity" value="forward" />
+      <output name="output" ftype="tabular" file="Read_Count_Lists.tab" />
+    </test>
+  </tests>
+</tool>
+