--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iit_store.xml	Tue Nov 08 13:26:41 2011 -0600
@@ -0,0 +1,188 @@
+<tool id="gmap_iit_store" name="GMAP IIT" version="2.0.0">
+  <description>Create a map store for known genes or SNPs</description>
+  <requirements>
+      <requirement type="binary">iit_store</requirement>
+      <!-- proposed tag for added datatype dependencies -->
+      <requirement type="datatype">gmap_annotation</requirement>
+      <requirement type="datatype">gmap_snps</requirement>
+      <requirement type="datatype">iit</requirement>
+      <requirement type="datatype">splicesites.iit</requirement>
+      <requirement type="datatype">introns.iit</requirement>
+      <requirement type="datatype">snps.iit</requirement>
+  </requirements>
+  <version_string>iit_store --version</version_string>
+  <command interpreter="command"> /bin/bash $shscript 2> $log </command>
+  <inputs>
+    <!-- Input data -->
+    <conditional name="map">
+      <param name="type" type="select" label="Make map for" >
+        <option value="genes">Introns and Splice sites</option>
+        <option value="snps">SNPs</option>
+        <option value="gmap">GMAP Annotation</option>
+      </param>
+      <when value="genes">
+        <conditional name="src">
+          <param name="src_format" type="select" label="Add splice and intron info from" >
+            <option value="refGeneTable">refGenes table from UCSC table browser</option>
+            <option value="gtf">GTF</option>
+            <option value="gff3">GFF3</option>
+          </param>
+          <when value="refGeneTable">
+            <param name="genes" type="data" format="tabular" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" />
+            <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" 
+                   help="Note that alignment tracks in UCSC sometimes have an extra column on the left.">
+              <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/>
+            </param>
+          </when>
+          <when value="gtf">
+            <param name="genes" type="data" format="gtf" label="Genes as GTF" help="" />
+          </when>
+          <when value="gff3">
+            <param name="genes" type="data" format="gff3" label="Genes in GFF3 format" help="" />
+          </when>
+        </conditional> 
+        <param name="maps" type="select" display="checkboxes" multiple="true" force_select="true" label="Add splice and intron info from" >
+          <option value="splicesites" selected="true">splicesites.iit</option>
+          <option value="introns" selected="false">introns.iit</option>
+        </param>
+      </when>
+      <when value="snps">
+        <conditional name="src">
+          <param name="src_format" type="select" label="Add SNP info from" >
+            <option value="snpTable">UCSC SNP Table</option>
+            <option value="snpFile">GMAP SNP File</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" optional="true" label="GMAP SNPs file" 
+               help="Format (3 columns):&lt;B&gt;
+                    &lt;br&gt;>rs62211261 21:14379270 CG
+                    &lt;br&gt;>rs62211262 21:14379281 CG
+                    &lt;/B&gt;
+                    &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>
+        </conditional> 
+      </when>
+      <when value="gmap">
+        <param name="annotation" type="data" format="gmap_annotation" label="GMAP mapfile" 
+          help="Format (2 or columns): &lt;B&gt;
+                &lt;br&gt;>label coords optional_tag
+                &lt;br&gt;optional_annotation (which may be zero, one, or multiple lines)
+                &lt;/B&gt;
+                &lt;br&gt;Each line must start with a &gt; character, then be followed by an identifier (which may have duplicates).  
+                &lt;br&gt;Then there should be the chromosomal coordinate range.  (Coordinates are all 1-based, so the first character of a chromosome is number 1.)  
+                &lt;br&gt;The coords should be of the form
+                &lt;br&gt; chr:position
+                &lt;br&gt;  chr:startposition..endposition
+                &lt;br&gt;The term chr:position is equivalent to chr:position..position.  
+                &lt;br&gt;If you want to indicate that the interval is on the minus strand or reverse direction, then endposition may be less than startposition.  
+                " />
+      </when>
+    </conditional> 
+  </inputs>
+  <outputs>
+    <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
+    <data format="splicesites.iit" name="splicesites_iit" label="${tool.name} on ${on_string} splicesites.iit">
+      <filter>(map['type'] == 'genes' and 'splicesites' in map['maps'])</filter>
+    </data>
+    <data format="introns.iit" name="introns_iit" label="${tool.name} on ${on_string} introns.iit">
+      <filter>(map['type'] == 'genes' and 'introns' in map['maps'])</filter>
+    </data>
+    <data format="snps.iit" name="snps_iit" label="${tool.name} on ${on_string} snps.iit">
+      <filter>(map['type'] == 'snps')</filter>
+    </data>
+    <data format="iit" name="map_iit" label="${tool.name} on ${on_string} map.iit">
+      <filter>(map['type'] == 'gmap')</filter>
+    </data>
+  </outputs>
+  <configfiles>
+    <configfile name="shscript">
+#!/bin/bash
+#set $catcmd = 'gzcat -f'
+#set $catcmd = 'cat'
+#set $ds = chr(36)
+#set $gt = chr(62)
+#set $lt = chr(60)
+#set $ad = chr(38)
+#set $ep = chr(33)
+#set $toerr = ''.join([$gt,$ad,'2'])
+#import os.path
+#if $map.type == 'genes':
+if [ $ep -e $map.src.genes ]; then echo "$map.src.genes does not exist" $toerr; exit 1; fi
+if [ $ep -s $map.src.genes ]; then echo "$map.src.genes is empty" $toerr; exit 2; fi
+ #if $map.src.src_format == 'refGeneTable':
+  #if 'splicesites' in [ $map.maps.__str__ ]:
+   $catcmd $map.src.genes | psl_splicesites -s $map.src.col_skip | iit_store -o  $splicesites_iit
+  #end if
+  #if 'introns' in [ $map.maps.__str__ ]:
+   $catcmd  $map.src.genes | psl_introns -s $map.src.col_skip | iit_store -o  $introns_iit
+  #end if
+ #elif $map.src.src_format == 'gtf':
+  #if 'splicesites' in [ $map.maps.__str__ ]:
+   $catcmd $map.src.genes | gtf_splicesites | iit_store -o  $splicesites_iit
+  #end if
+  #if 'introns' in [ $map.maps.__str__ ]:
+   $catcmd $map.src.genes | gtf_introns | iit_store -o  $introns_iit
+  #end if
+ #elif $map.src.src_format == 'gff3':
+  #if 'splicesites' in [ $map.maps.__str__ ]:
+   $catcmd $map.src.genes | gff3_splicesites | iit_store -o  $splicesites_iit
+  #end if
+  #if 'introns' in [ $map.maps.__str__ ]:
+   $catcmd $map.src.genes | gff3_introns | iit_store -o  $introns_iit
+  #end if
+ #end if
+#elif $map.type == 'snps':
+if [ $ep -s $map.src.snps ]; then echo "$map.src.snps is empty" $toerr; exit 2; fi
+ #if $map.src.snpsex.__str__ != 'None':
+  $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight -e $map.src.snpsex | iit_store -o  $snps_iit
+ #else:
+  $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight | iit_store -o $snps_iit 
+ #end if
+#else:
+  $catcmd $map.src.snps | iit_store -o $map_iit 
+#end if
+    </configfile>
+  </configfiles>
+
+  <tests>
+  </tests> 
+
+  <help>
+
+
+**iit_store**
+
+GMAP IIT creates an Interval Index Tree map of known splice sites, introns, or SNPs (it uses iit_store described in the GMAP documentation).  The maps can be used in GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program).  Maps are typically used for known splice sites, introns, or SNPs.  
+
+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
+
+
+**inputs**
+
+  </help>
+</tool>
+