--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GSnap.xml	Tue Sep 13 00:51:38 2011 -0400
@@ -0,0 +1,102 @@
+<tool id="GSnap" name="GSnap" version="">
+  <description>RNA aligner</description>
+  <parallelism method="basic"></parallelism>
+  <command interpreter="python">
+    GSnap.py
+    
+      #if $advanced_condition.advanced == 'True':
+        -t "$advanced_condition.threads"
+        -B "$advanced_condition.memkeep"
+      #else:
+        -t 4
+        -B 4
+      #end if
+    
+      -D "${filter(lambda x: str(x[0]) == str($reference), $__app__.tool_data_tables['GSnap_indexes'].get_fields())[0][-1]}"
+  
+      -A "$format"
+      -d "$reference"
+       "$input1"
+       "$input2"
+      > $output
+  
+      2> $error
+  
+  </command>
+  <requirements>
+    <requirement type='package'>gsnap</requirement>
+  </requirements>
+  <inputs>
+    <param name="format" type="select" label="Output format" help="">
+    
+      <option value="sam" >sam</option>
+      <option value="fasta" >fasta</option>
+    </param>
+    <param name="reference" type="select" label="The reference database" help="">
+    <options from_data_table="gsnap_indexes" />
+    </param>
+    <param name="input1" type="data" label="Paired end 1" help="Your input." format="fastq" />
+    <param name="input2" type="data" label="Paired end 2" help="Your input." format="fastq" />
+    <conditional name='advanced_condition'>
+  	  <param name='advanced' type='select' label="Advanced options for GSnap">
+        <option value='False' selected='selected'>False</option>
+        <option value='True'>True</option>
+  	  </param>
+  	  <when value='False' />
+  	  <when value='True'>
+        <param name="threads" type="integer" label="Number of threads" help="Leave this alone." value="4" />
+        <param name="memkeep" type="integer" label="Keep maps in memory" help="Leave this alone." value="4" />
+  	  </when>
+  	</conditional>
+  </inputs>
+  <outputs>
+    <data name="output" label="${tool.name} on ${on_string}: output" format="txt" >
+        <change_format>
+          <when input="format" value="sam" format="sam" />
+        
+          <when input="format" value="fasta" format="fasta" />
+        </change_format>
+        </data>
+  
+    <data name="error" label="${tool.name} on ${on_string}: Error/Status message." format="txt" ></data>
+  
+  </outputs>
+  <help>
+**What it does**
+
+BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60.
+
+------
+
+**Know what you are doing**
+
+.. class:: warningmark
+
+There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
+
+ .. __: http://bio-bwa.sourceforge.net/
+
+------
+
+**Input formats**
+
+BWA accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
+
+
+
+------
+
+**Generated By**: 
+
+LUMC Interface Generator (0.1)      
+
+2011-09-13T04:45:57.634566Z
+
+**Based On**:
+
+RDF Definition of "GSnap"                                                  
+
+2011-08-29T12:07:31.688276Z                                                
+
+  </help>
+</tool>
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