--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stampy_wrapper.xml	Wed Dec 17 10:16:18 2014 -0500
@@ -0,0 +1,132 @@
+<tool id="Stampy" name="Stampy" version="1.0.21">
+    <description>is a package for mapping of short reads from illumina sequencing machines onto a reference genome</description>
+     <command interpreter="python">  stampy_wrapper.py 
+
+      ## Indexing of the reference genome
+      --assembly=$Assembly 
+      --species=$species
+      --genome_index=$G 
+      --output=$output
+
+      ## Reference genome for creating index
+      --genome=$input
+      #if $refGenomeSource.genomeSource == "indexed":
+      --genome1="${refGenomeSource.index.fields.path}"
+      #end if
+      ## input file for single paired read
+          --input1=$input1
+        
+        ## Second input only if input is paired-end.
+        #if $singlePaired.sPaired == "paired"
+            --input1=$singlePaired.input1 
+            --input2=$singlePaired.input2
+        #end if
+     ## Parameters
+      --settings=$params.settingsType
+   	#if $params.settingsType == "full":
+        --sd=${params.d}
+   	--insert=${params.i}
+   	--subrate=${params.r}
+       	#end if  
+     </command>
+    <inputs>
+        <param name="Assembly" type="text" value=""/>
+	<param name="species" type="text" value=""/>
+        <param name="G" type="text" value=""/>
+
+       <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" selected="true">Use one from the history</option>
+          </param>
+          <when value="indexed">
+             <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+              <options from_file="stampy_indices.loc">
+                 <column name ="value" index="0" />
+                 <column name ="name" index="1" />
+              </options>
+        </param>
+          </when>
+          <when value="history">hg18_
+            <param name="input" type="data" format="fna" metadata_name="dbkey" label="Select the reference genome" />
+          </when> 
+        
+        </conditional>  
+        <conditional name="singlePaired">
+            <param name="sPaired" type="select" label="Is this library mate-paired?">
+              <option value="single">Single-end</option>
+              <option value="paired">Paired-end</option>
+            </param>
+            <when value="single">
+                <param format="fna" name="input1" type="data" label="Input sequence" />
+            </when>
+            <when value="paired">
+                <param format="fna" name="input1" type="data" label="Input sequence"  />
+                <param format="fna" name="input2" type="data" label="Input sequence"  />
+            </when>
+        </conditional>
+        <conditional name="params">
+            <param name="settingsType" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for the parameters.">
+              <option value="preSet">Use Defaults</option>
+              <option value="full">Full parameter list</option>
+            </param>
+            <when value="preSet" />
+            <!-- Full/advanced parameters. -->
+            <when value="full">
+        <param name="i" type="text" value="250" label="Insert size" />
+        <param name="d" type="text" value="50" label="standard deviation" />
+        <param name="r" type="text" value="0.001" label="substitutionrate" />
+ 	</when>  <!-- full -->
+      </conditional>  <!-- params -->
+
+    </inputs>
+
+<outputs>
+    <data format="txt" name="output" label="outfile"/>
+</outputs>
+<help>
+**Stampy**
+
+Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome (http://www.well.ox.ac.uk/project-stampy). Selected options used here are given below
+
+------
+
+**Indexing usage**
+
+*Building index*
+
+stampy.py --species=human --assembly=hg18_ncbi36 -G hg18 /data/genomes/hg18/*.fa.gz
+
+*Building hash*
+
+stampy.py -g hg18 -H hg18
+
+------
+
+
+**Alignment usage**
+
+ stampy.py options -g hg18 -h hg18 -M reads_1.fastq reads_2.fastq
+
+
+------
+
+**Options - Description**
+
+--insertsize
+
+Set the mean insert size for paired-end reads (default: 250)
+
+--insertsd=N                 
+
+Set the standard deviation of the insert size distribution (default: 60)
+
+--substitutionrate=S		 
+
+ Introduce an expected fraction S of Poisson-distributed substitutions  (default: 0.001)
+
+
+</help>
+
+</tool>
+