--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpindex.xml	Tue Nov 08 13:26:41 2011 -0600
@@ -0,0 +1,141 @@
+<tool id="gmap_snpindex" name="GMAP SNP Index" version="2.0.0">
+  <description>build index files for known SNPs</description>
+  <requirements>
+      <requirement type="binary">snpindex</requirement>
+      <!-- proposed tag for added datatype dependencies -->
+      <requirement type="datatype">gmapsnpindex</requirement>
+      <requirement type="datatype">gmapdb</requirement>
+      <requirement type="datatype">gmap_snps</requirement>
+      <requirement type="datatype">snps.iit</requirement>
+  </requirements>
+  <version_string>snpindex --version</version_string>
+  <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command>
+  <inputs>
+    <conditional name="refGenomeSource">
+     <param name="genomeSource" type="select" label="Will you map to 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="gmapdb">Use gmapdb from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
+          <options from_file="gmap_indices.loc">
+            <column name="uid" index="0" />
+            <column name="dbkey" index="1" />
+            <column name="name" index="2" />
+            <column name="kmers" index="3" />
+            <column name="maps" index="4" />
+            <column name="snps" index="5" />
+            <column name="value" index="6" />
+          </options>
+        </param>
+      </when>
+      <when value="gmapdb">
+        <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" 
+              help="A GMAP database built with GMAP Build"/>
+      </when>
+    </conditional>
+    <conditional name="dbsnp">
+      <param name="snp_source" type="select" label="Add SNP info from" >
+        <option value="snpTable">UCSC SNP Table</option>
+        <option value="snpFile">GMAP SNP File</option>
+        <option value="snpIIT">"GMAP SNPs map from GMAP iit store</option>
+      </param>
+      <when value="snpTable">
+        <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" />
+        <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" />
+        <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">
+          <option value="1" selected="true">1 (High)</option>
+          <option value="2">2 (Medium)</option>
+          <option value="3">3 (All)</option>
+        </param>
+      </when>
+      <when value="snpFile">
+        <param name="snps" type="data" format="gmap_snps" label="GMAP SNPs file" 
+           help="Format (3 columns):
+                &lt;br&gt;>rs62211261 21:14379270 CG
+                &lt;br&gt;>rs62211262 21:14379281 CG
+                &lt;br&gt;Each line must start with a &gt; character, then be followed by an
+                identifier (which may have duplicates).  Then there should be the
+                chromosomal coordinate of the SNP.  (Coordinates are all 1-based, so
+                the first character of a chromosome is number 1.)  Finally, there
+                should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN)
+                &lt;br&gt;These alleles must correspond to the possible nucleotides on the plus strand of the genome.  
+                If the one of these two letters does not match the allele in the reference
+                sequence, that SNP will be ignored in subsequent processing as a probable error.
+                The N stands for any other allele." />
+      </when>
+      <when value="snpIIT">
+        <param name="snpIIT" type="data" format="snps.iit" label="GMAP SNPs map" help="Created by: GMAP iit store" />
+      </when>
+    </conditional> 
+    <param name="snps_name" type="text" value="snps" label="Name for this SNP index" help="no white space characters">
+    </param>
+  </inputs>
+  <outputs>
+    <!--
+    <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
+    -->
+    <data format="gmapsnpindex" name="output" label="${tool.name} on ${on_string} snpindex" />
+  </outputs>
+  <configfiles>
+    <configfile name="shscript">
+#!/bin/bash
+#set $ds = chr(36)
+#set $gt = chr(62)
+#set $lt = chr(60)
+#set $ad = chr(38)
+#import os.path
+#if $refGenomeSource.genomeSource == "gmapdb":
+#set $gmapdb = $refGenomeSource.gmapdb.extra_files_path
+#set $refname = $refGenomeSource.gmapdb.metadata.db_name
+#else:
+#set $gmapdb = $os.path.dirname($refGenomeSource.gmapindex.value) 
+$refname = $os.path.basename($refGenomeSource.gmapindex.value)
+#end if
+#set $gmapsnpdir = $output.extra_files_path
+mkdir -p $gmapsnpdir
+#set $snpsname = $snps_name.__str__
+#set $snpsiit = '.'.join([$snpsname,'iit'])
+#set $pathsnps = $os.path.join($gmapsnpdir,$snpsname)
+#set $pathsnpsiit = $os.path.join($gmapsnpdir,$snpsiit)
+#if $dbsnp.snp_source != 'none' and $dbsnp.snps.__str__ != 'None':
+#if $dbsnp.snp_source == 'snpTable':
+#if $dbsnp.snpsex.__str__ != 'None':
+cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex | iit_store -o $pathsnps
+#else:
+cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight | iit_store -o $pathsnps
+#end if
+#elif $dbsnp.snp_source == 'snpFile':
+cat $dbsnp.snps | iit_store -o $pathsnps
+#elif $dbsnp.snp_source == 'snpIIT':
+cat $dbsnp.snps  > $pathsnpsiit
+#end if
+snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
+echo snpindex -D  $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
+#end if
+    </configfile>
+  </configfiles>
+
+  <tests>
+  </tests> 
+
+  <help>
+
+
+**GMAP SNP Index**
+
+GMAP SNP Index (snpindex in the GMAP documentaion) creates an index for known SNPs allowing for SNP tolerant mapping and alignment when using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program).  
+
+You will want to read the README_
+
+Publication_ citation: Thomas D. Wu, Colin K. Watanabe  Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
+
+.. _GMAP: http://research-pub.gene.com/gmap/
+.. _GSNAP: http://research-pub.gene.com/gmap/
+.. _README: http://research-pub.gene.com/gmap/src/README
+.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
+
+
+  </help>
+</tool>
+