# HG changeset patch
# User jjohnson
# Date 1343737186 14400
# Node ID 6adc485b6dc073e0defd6dd232840fb563923f34
# Parent  93911bac43da3c97cc9b6ac492e0e83ce7ee19de
Uploaded

diff -r 93911bac43da -r 6adc485b6dc0 README
--- a/README	Thu Jan 05 14:31:24 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-GMAP applications and citation info are available from:    http://research-pub.gene.com/gmap/
-
-
-    Installation instructions are in the README file in the download, 
-    and online:   http://research-pub.gene.com/gmap/src/README
-
-    These tools were consistent with gmap version: 2011-11-30
-
-
-GMAP and  GSNAP use added datatypes:
-
-   add datatype definition file: lib/galaxy/datatypes/gmap.py
-
-   add the following import line to:  lib/galaxy/datatypes/registry.py
-   import gmap # added for gmap tools
-
-   add to datatypes_conf.xml
-        <!-- Start GMAP Datatypes -->
-        <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB"  display_in_upload="False"/>
-        <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex"  display_in_upload="False"/>
-        <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="tally.iit" type="galaxy.datatypes.gmap:TallyIntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation"  display_in_upload="False"/>
-        <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation"  display_in_upload="True"/>
-        <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation"  display_in_upload="True"/>
-        <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation"  display_in_upload="True"/>
-        <datatype extension="gsnap_tally" type="galaxy.datatypes.gmap:TallyAnnotation"  display_in_upload="True"/>
-        <datatype extension="gsnap" type="galaxy.datatypes.gmap:GsnapResult"  display_in_upload="True"/>
-        <!-- End GMAP Datatypes -->
-
-Tools:
-  GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations
-  GMAP - map sequences to a reference sequence GmapDB index
-  GSNAP - align sequences to a reference and detect splicing 
-
-  Add to  tool_conf.xml     ( probably in the "NGS: Mapping" section )
-   <tool file="gmap/gmap.xml" />
-   <tool file="gmap/gsnap.xml" />
-   <tool file="gmap/gmap_build.xml" />
-   <tool file="gmap/snpindex.xml" />
-   <tool file="gmap/iit_store.xml" />
-
-Admin built cached gmapdb indexes defined in tool-data/gmap_indices.loc
-
-
-TODO:
-  
-  
-  Add classes to gmap.py
-    CmetIndex - an index created by cmetindex
-    AtoiIndex - an index created by atoiindex
-
-  Add tally creation
-    gsnap default output -> gsnap_tally -> iit_store
-
-  Add goby support
-    Should add separate tools and datatypes for goby 
-    GSNAP goby output relies on goby input, might be better to have a separate gsnap tool for goby
-
-  Possibly add Tools:
-    get_genome - retrieves from a gmapdb
-    cmetindex - create methylcytosine index
-    atoiindex - create  A-to-I RNA editing index
-    
-    
-     
-
-	
diff -r 93911bac43da -r 6adc485b6dc0 gmap.xml
--- a/gmap.xml	Thu Jan 05 14:31:24 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,482 +0,0 @@
-<tool id="gmap" name="GMAP" version="2.0.1">
-  <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description>
-  <requirements>
-    <requirement type="binary">gmap</requirement>
-  </requirements>
-  <version_string>gmap --version</version_string>
-  <command>
-    #import os,os.path
-    gmap
-    --nthreads=4 --ordered
-    #if $refGenomeSource.genomeSource == "history":
-      --gseg=$refGenomeSource.ownFile
-    #elif $refGenomeSource.genomeSource == "gmapdb":
-      #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0]
-      --dir=$refGenomeSource.gmapdb.extra_files_path --db=$gmapdb
-      #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:
-        --kmer=$refGenomeSource.kmer
-      #end if
-    #else:
-      --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value)
-      #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:
-        --kmer=$refGenomeSource.kmer
-      #end if
-    #end if
-    #if $result.format == "summary":
-      --summary
-    #elif $result.format == "align":
-      --align
-    #elif $result.format == "continuous":
-      --continuous
-    #elif $result.format == "continuous-by-exon":
-      --continuous-by-exon
-    #elif $result.format == "compress":
-      --compress
-    #elif $result.format == "exons_dna":
-      --exons=cdna
-    #elif $result.format == "exons_gen":
-      --exons=genomic
-    #elif $result.format == "protein_dna":
-      --protein_dna
-    #elif $result.format == "protein_gen":
-      --protein_gen
-    #elif $result.format == "sam":
-      --format=$result.sam_paired_read
-      $result.no_sam_headers 
-      #* Removed in gmap version 2011-11-30
-      #if len($result.noncanonical_splices.__str__) > 0
-         --noncanonical-splices=$result.noncanonical_splices
-      #end if
-      *#
-      #if len($result.read_group_id.__str__) > 0
-         --read-group-id=$result.read_group_id
-      #end if
-      #if len($result.read_group_name.__str__) > 0
-         --read-group-name=$result.read_group_name
-      #end if
-      #if len($result.read_group_library.__str__) > 0
-         --read-group-library=$result.read_group_library
-      #end if
-      #if len($result.read_group_platform.__str__) > 0
-         --read-group-platform=$result.read_group_platform
-      #end if
-    #elif $result.format != "gmap":
-      --format=$result.format
-    #end if
-    #if $computation.options == "advanced":
-      $computation.nosplicing
-      $computation.cross_species
-      #if len($computation.min_intronlength.__str__) > 0
-        --min-intronlength=$computation.min_intronlength
-      #end if
-      #if len($computation.intronlength.__str__) > 0
-        --intronlength=$computation.intronlength
-      #end if
-      #if len($computation.localsplicedist.__str__) > 0
-        --localsplicedist=$computation.localsplicedist
-      #end if
-      #if len($computation.totallength.__str__) > 0
-        --totallength=$computation.totallength
-      #end if
-      #if len($computation.trimendexons.__str__) > 0
-        --trimendexons=$computation.trimendexons
-      #end if
-      --direction=$computation.direction
-      --canonical-mode=$computation.canonical
-      --prunelevel=$computation.prunelevel
-      --allow-close-indels=$computation.allow_close_indels
-      #if len($computation.microexon_spliceprob.__str__) >= 0:
-        --microexon-spliceprob=$computation.microexon_spliceprob
-      #end if
-      #if len($computation.chimera_margin.__str__) >= 0:
-        --chimera-margin=$computation.chimera_margin
-      #end if
-    #end if
-    #if $advanced.options == "used":
-      #if len($advanced.npaths.__str__) > 0:
-        --npaths=$advanced.npaths
-      #end if
-      #if len($advanced.suboptimal_score.__str__) > 0:
-        --suboptimal-score=$advanced.suboptimal_score
-      #end if
-      #if len($advanced.chimera_overlap.__str__) > 0:
-        --chimera_overlap=$advanced.chimera_overlap
-      #end if
-      $advanced.protein
-      $advanced.tolerant
-      $advanced.nolengths
-      $advanced.invertmode
-      #if len($advanced.introngap.__str__) > 0:
-        --introngap=$advanced.introngap
-      #end if
-      #if len($advanced.wraplength.__str__) > 0:
-        --wraplength=$advanced.wraplength
-      #end if
-    #end if
-    #if $split_output == True
-      $split_output
-    #end if
-    #if len($quality_protocol.__str__) > 0:
-      --quality-protocol=$quality_protocol
-    #end if
-    $input
-    #for $i in $inputs:
-      ${i.added_input}
-    #end for
-    #if $split_output == True
-      2> $gmap_stderr 
-    #else
-      2> $gmap_stderr > $output
-    #end if
-  </command>
-  <inputs>
-    <!-- Input data -->
-    <param name="input" type="data" format="fasta,fastqsanger,fastqillumina" label="&lt;H2&gt;Input Sequences&lt;/H2&gt;Select an mRNA or EST dataset to map" />
-    <repeat name="inputs" title="addtional mRNA or EST dataset to map">
-      <param name="added_input" type="data" format="fasta,fastqsanger,fastqillumina" label=""/>
-    </repeat>
-    <param name="quality_protocol" type="select" label="Protocol for input quality scores">
-      <option value="">No quality scores</option>
-      <option value="sanger">Sanger quality scores</option>
-      <option value="illumina">Illumina quality scores</option>
-    </param>
-
-    <!-- GMAPDB for mapping -->
-    <conditional name="refGenomeSource">
-     <param name="genomeSource" type="select" label="&lt;HR&gt;&lt;H2&gt;Map To&lt;/H2&gt;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>
-        <option value="history">Use a fasta reference sequence 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>
-        <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size">
-          <options from_file="gmap_indices.loc">
-            <column name="name" index="3"/>
-            <column name="value" index="3"/>
-            <filter type="param_value" ref="gmapindex" column="6"/>
-            <filter type="multiple_splitter" column="3" separator=","/>
-            <filter type="add_value" name="" value=""/>
-            <filter type="sort_by" column="3"/>
-          </options>
-        </param>
-        <param name="map" type="select" data_ref="gmapindex" label="Look for splicing involving known sites or known introns" help="">
-          <options from_file="gmap_indices.loc">
-            <column name="name" index="4"/>
-            <column name="value" index="4"/>
-            <filter type="param_value" ref="gmapindex" column="6"/>
-            <filter type="multiple_splitter" column="4" separator=","/>
-            <filter type="add_value" name="" value=""/>
-            <filter type="sort_by" column="4"/>
-          </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"/>
-        <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size">
-          <options>
-            <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/>
-          </options>
-        </param>
-        <param name="map" type="select"  data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help="">
-          <options>
-            <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/>
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" 
-              help="Fasta containing genomic DNA sequence"/>
-      </when>
-    </conditional>
-
-    
-    <!-- Computation options -->
-    <conditional name="computation">
-      <param name="options" type="select" label="&lt;HR&gt;Computational Settings" help="">
-        <option value="default">Use default settings</option>
-        <option value="advanced">Set Computation Options</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-       <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/>
-       <param name="min_intronlength" type="integer" value="" optional="true" label="Min length for one internal intron (default 9)." help="Below this size, a genomic gap will be considered a deletion rather than an intron." >	
-         <validator type="in_range" message="min_intronlength must be positive" min="0" />
-       </param>
-       <param name="intronlength" type="integer" value="" optional="true" label="Max length for one intron (default 1000000)" >	
-         <validator type="in_range" message="intronlength must be positive" min="0" />
-       </param>
-       <param name="localsplicedist" type="integer" value="" optional="true" label="Max length for known splice sites at ends of sequence (default 200000)" >	
-         <validator type="in_range" message="localsplicedist must be positive" min="0" />
-       </param>
-       <param name="totallength"  type="integer" value="" optional="true" label="Max total intron length (default 2400000)" >	
-         <validator type="in_range" message="totallength must be positive" min="0" />
-       </param>
-       <param name="chimera_margin" type="integer" value="" optional="true" label="Amount of unaligned sequence that triggers search for a chimera" 
-              help=" default is 40, To turn off, set to a large value (greater than the query length)" >	
-         <validator type="in_range" message="chimera_margin must be positive" min="0" />
-       </param>
-       <param name="direction"  type="select" label="cDNA direction">	
-         <option value="auto">auto</option>
-         <option value="sense_force">sense_force</option>
-         <option value="antisense_force">antisense_force</option>
-         <option value="sense_filter">sense_filter</option>
-         <option value="antisense_filter">antisense_filter</option>
-       </param>
-       <param name="trimendexons"  type="integer" value="" optional="true" label="Trim end exons with fewer than given number of matches (in nt, default 12)" >	
-         <validator type="in_range" message="trimendexons must be positive" min="1" />
-       </param>
-       <param name="cross_species" type="boolean" truevalue="--cross-species" falsevalue="" checked="false" label="Cross-species alignment" help="For cross-species alignments, use a more sensitive search for canonical splicing"/>
-       
-       <param name="canonical"  type="select" label="Reward for canonical and semi-canonical introns">	
-         <option value="1">high reward (default)</option>
-         <option value="0">low reward</option>
-         <option value="2">low reward for high-identity sequences</option>
-       </param>
-       <param name="allow_close_indels"  type="select" label="Allow an insertion and deletion close to each other">	
-         <option value="1" selected="true">yes (default)</option>
-         <option value="0">no</option>
-         <option value="2">only for high-quality alignments</option>
-       </param>
-       <param name="microexon_spliceprob" type="float" value="" optional="true" label="Micro Exon splice probablility threshold" 
-              help="Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90)" >	
-         <validator type="in_range" message="slice probability between 0.00 and 1.00" min="0" max="1"/> 
-       </param>
-       <param name="prunelevel"  type="select" label="Pruning level">	
-         <option value="0">no pruning (default)</option>
-         <option value="1">poor sequences</option>
-         <option value="2">repetitive sequences</option>
-         <option value="3">poor and repetitive sequences</option>
-       </param>
-       <!--  could do this as a config file 
-       <param name="chrsubsetfile" type="data" format="fasta" label="User-supplied chromosome subset file" />
-       <param name="chrsubset" type="text" label="Chromosome subset to search" />
-       -->
-      </when>
-    </conditional>
-
-    <!-- Advanced Settings -->
-    <conditional name="advanced">
-      <param name="options" type="select" label="&lt;HR&gt;Advanced Settings" help="">
-        <option value="default">Use default settings</option>
-        <option value="used">Set Options</option>
-      </param>
-      <when value="default"/>
-      <when value="used">
-       <param name="nolengths" type="boolean" checked="false" truevalue="--nolengths=true" falsevalue="" label="No intron lengths in alignment"/>
-       <param name="invertmode" type="select" label=" Mode for alignments to genomic (-) strand" help="">
-        <option value="">Don't invert the cDNA (default)</option>
-        <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option>
-        <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option>
-       </param>
-       <param name="introngap" type="integer" value="" optional="true" label="Nucleotides to show on each end of intron (default=3)">	
-         <validator type="in_range" message="introngap must be positive" min="0" />
-       </param>
-       <param name="wraplength" type="integer" value="" optional="true" label="Line Wrap length for alignment (default=50)">	
-         <validator type="in_range" message="wraplength must be positive" min="1" />
-       </param>
-       <param name="npaths" type="integer" value="" optional="true"
-              label="Maximum number of paths to show.  Ignored if negative.  If 0, prints two paths if chimera detected, else one." >	
-         <validator type="in_range" message="npaths must be positive" min="0" />
-       </param>
-       <param name="suboptimal_score" type="integer" value="" optional="true"
-              label="Report only paths whose score is within this value of the best path"
-              help="By default the program prints all paths found." >	
-         <validator type="in_range" message="suboptimal_score must be positive" min="0" />
-       </param>
-       <param name="chimera_overlap" type="integer" value="" optional="true" label="Overlap to show, if any, at chimera breakpoint (default 0)" >	
-                <validator type="in_range" message="chimera_overlap must be positive" min="0" />
-       </param>
-       <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue="" 
-              label="Translates cDNA with corrections for frameshifts"/>
-       <param name="protein" type="select" label="Protein alignment" help="">
-        <option value="">default</option>
-        <option value="--fulllength=true">Assume full-length protein, starting with Met</option>
-        <option value="--truncate=true">Truncate alignment around full-length protein, Met to Stop</option>
-       </param>
-      </when>
-    </conditional>
-
-    <!-- Output data -->
-    <conditional name="result">
-    <param name="format" type="select" label="&lt;HR&gt;&lt;H2&gt;Output&lt;/H2&gt;Select the output format" help="">
-      <option value="gmap">GMAP default output</option>
-      <option value="summary">Summary of alignments</option>
-      <option value="align">Alignment</option>
-      <option value="continuous">Alignment in three continuous lines</option>
-      <option value="continuous-by-exon">Alignment in three lines per exon</option>
-      <option value="compress">Print output in compressed format</option>
-      <option value="exons_dna">Print exons cDNA</option>
-      <option value="exons_gen">Print exons genomic</option>
-      <option value="protein_dna">Print protein sequence (cDNA)</option>
-      <option value="protein_gen">Print protein sequence (genomic)</option>
-      <option value="psl">PSL (BLAT) format</option>
-      <option value="gff3_gene">GFF3 gene format</option>
-      <option value="gff3_match_cdna">GFF3 match cDNA format</option>
-      <option value="gff3_match_est">GFF3 match EST format</option>
-      <option value="splicesites">splicesites output (for GSNAP)</option>
-      <option value="introns">introns output (for GSNAP)</option>
-      <option value="map_exons">IIT FASTA exon map format</option>
-      <option value="map_genes">IIT FASTA map format</option>
-      <option value="coords">coords in table format</option>
-      <option value="sam" selected="true">SAM format</option>
-    </param>
-      <when value="gmap">
-      </when>
-      <when value="summary"/>
-      <when value="align">
-      </when>
-      <when value="continuous">
-      </when>
-      <when value="continuous-by-exon">
-      </when>
-      <when value="compress"/>
-      <when value="exons_dna"/>
-      <when value="exons_gen"/>
-      <when value="protein_dna"/>
-      <when value="protein_gen"/>
-      <when value="psl"/>
-      <when value="gff3_gene"/>
-      <when value="gff3_match_cdna"/>
-      <when value="gff3_match_est"/>
-      <when value="splicesites"/>
-      <when value="introns"/>
-      <when value="map_exons"/>
-      <when value="map_genes"/>
-      <when value="coords"/>
-      <when value="sam">
-        <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/>
-        <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/>
-        <!--  Removed in gmap version 2011-11-30
-        <param name="noncanonical_splices" type="select" label="Print non-canonical genomic gaps greater than 20 nt in CIGAR string as STRING.">
-          <option value="">Use default</option>
-          <option value="N">N</option>
-          <option value="D">D</option>
-        </param>
-        -->
-        <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/>
-        <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/>
-        <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/>
-        <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/>
-      </when>
-    </conditional> <!-- name="result" -->
-
-    <param name="split_output" type="boolean" truevalue="--split-output=gmap_out" falsevalue="" checked="false" label="Separate outputs for nomapping, uniq, mult, and chimera" help="(chimera only when chimera-margin is selected)"/>
-
-
-    <!-- 
-      map=iitfile      Map file.  If argument is '?' (with the quotes), this lists available map files.
-      mapexons         Map each exon separately
-      mapboth          Report hits from both strands of genome
-      flanking=INT     Show flanking hits (default 0)
-      print-comment    Show comment line for each hit
-    -->
-
-
-  </inputs>
-  <outputs>
-    <data format="txt" name="gmap_stderr" label="${tool.name} on ${on_string}: stderr"/>
-    <data format="txt" name="output" label="${tool.name} on ${on_string} ${result.format}" >
-      <filter>(split_output == False)</filter>
-      <change_format>
-        <when input="result['format']" value="gff3_gene" format="gff3"/>
-        <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
-        <when input="result['format']" value="gff3_match_est" format="gff3"/>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
-        <when input="result['format']" value="introns" format="gmap_introns"/>
-        <when input="result['format']" value="map_genes" format="gmap_annotation"/>
-        <when input="result['format']" value="map_exons" format="gmap_annotation"/>
-      </change_format>
-    </data>
-    <data format="txt" name="uniq" label="${tool.name} on ${on_string} uniq.${result.format}"  from_work_dir="gmap_out.uniq">
-      <filter>(split_output == True)</filter>
-      <change_format>
-        <when input="result['format']" value="gff3_gene" format="gff3"/>
-        <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
-        <when input="result['format']" value="gff3_match_est" format="gff3"/>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
-        <when input="result['format']" value="introns" format="gmap_introns"/>
-        <when input="result['format']" value="map_genes" format="gmap_annotation"/>
-        <when input="result['format']" value="map_exons" format="gmap_annotation"/>
-      </change_format>
-    </data>
-    <data format="txt" name="transloc" label="${tool.name} on ${on_string} transloc.${result.format}"  from_work_dir="gmap_out.transloc">
-      <filter>(split_output == True)</filter>
-      <change_format>
-        <when input="result['format']" value="gff3_gene" format="gff3"/>
-        <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
-        <when input="result['format']" value="gff3_match_est" format="gff3"/>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
-        <when input="result['format']" value="introns" format="gmap_introns"/>
-        <when input="result['format']" value="map_genes" format="gmap_annotation"/>
-        <when input="result['format']" value="map_exons" format="gmap_annotation"/>
-      </change_format>
-    </data>
-    <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}"  from_work_dir="gmap_out.nomapping">
-      <filter>(split_output == True)</filter>
-      <change_format>
-        <when input="result['format']" value="gff3_gene" format="gff3"/>
-        <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
-        <when input="result['format']" value="gff3_match_est" format="gff3"/>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
-        <when input="result['format']" value="introns" format="gmap_introns"/>
-        <when input="result['format']" value="map_genes" format="gmap_annotation"/>
-        <when input="result['format']" value="map_exons" format="gmap_annotation"/>
-      </change_format>
-    </data>
-    <data format="txt" name="mult" label="${tool.name} on ${on_string} mult.${result.format}"  from_work_dir="gmap_out.mult">
-      <filter>(split_output == True)</filter>
-      <change_format>
-        <when input="result['format']" value="gff3_gene" format="gff3"/>
-        <when input="result['format']" value="gff3_match_cdna" format="gff3"/>
-        <when input="result['format']" value="gff3_match_est" format="gff3"/>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="splicesites" format="gmap_splicesites"/>
-        <when input="result['format']" value="introns" format="gmap_introns"/>
-        <when input="result['format']" value="map_genes" format="gmap_annotation"/>
-        <when input="result['format']" value="map_exons" format="gmap_annotation"/>
-      </change_format>
-    </data>
-  </outputs>
-  <tests>
-  </tests> 
-
-  <help>
-
-**What it does**
-
-GMAP_ (Genomic Mapping and Alignment Program)  The functionality provided by gmap allows a user to: (1) map and align a single cDNA interactively against a large genome in about a second, without the startup time of several minutes typically needed by existing mapping programs; (2) switch arbitrarily among different genomes, without the need for a preloaded server dedicated to each genome; (3) run the program on computers with as little as 128 MB of RAM (random access memory); (4) perform high-throughput batch processing of cDNAs by using memory mapping and multithreading when appropriate memory and hardware are available; (5) generate accurate gene models, even in the presence of substantial polymorphisms and sequence errors; (6) locate splice sites accurately without the use of probabilistic splice site models, allowing generalized use of the program across species; (7) detect statistically significant microexons and incorporate them into the alignment; and (8) handle mapping and alignment tasks on genomes having alternate assemblies, linkage groups or strains.  It is developed by Thomas D. Wu of Genentech, Inc.  
-
-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/
-.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
-
-------
-
-**Know what you are doing**
-
-.. class:: warningmark
-
-You will want to read the README_
-
-.. _README: http://research-pub.gene.com/gmap/src/README
-
-  </help>
-</tool>
-
diff -r 93911bac43da -r 6adc485b6dc0 gmap_build.xml
--- a/gmap_build.xml	Thu Jan 05 14:31:24 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,174 +0,0 @@
-<tool id="gmap_build" name="GMAP Build" version="2.0.0">
-  <description>a database genome index for GMAP and GSNAP</description>
-  <requirements>
-      <requirement type="binary">gmap_build</requirement>
-  </requirements>
-  <version_string>gmap --version</version_string>
-  <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command>
-  <inputs>
-    <!-- Name for this gmapdb -->
-    <param name="refname" type="text" label="Name you want to give this gmap database" help="">
-      <validator type="empty_field" message="A database name is required."/>
-    </param>
-    <!-- Input data -->
-    <repeat name="inputs" title="Reference Sequence" min="1">
-      <param name="input" type="data" format="fasta" label="reference sequence fasta" />
-    </repeat>
-
-    <param name="kmer" type="select" multiple="true" force_select="true" label="kmer size" help="">
-      <option value="12">12</option>
-      <option value="13">13</option>
-      <option value="14">14</option>
-      <option value="15" selected="true">15</option>
-    </param>  
-    <param name="cmetindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create cmetindex to process reads from bisulfite-treated DNA"/>
-    <param name="atoiindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create atoiindex to process reads under RNA-editing tolerance"/>
-    <conditional name="splicesite">
-      <param name="splice_source" type="select" label="Add splice and intron info from" >
-        <option value="none"></option>
-        <option value="refGeneTable">refGenes table from UCSC table browser</option>
-        <option value="gtf">GTF</option>
-        <option value="gff3">GFF3</option>
-      </param>
-      <when value="none"/>
-      <when value="refGeneTable">
-        <param name="refGenes" type="data" format="tabular" optional="true" 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="gtfGenes" type="data" format="gtf" optional="true" label="Genes as GTF" help="" />
-      </when>
-      <when value="gff3">
-        <param name="gff3Genes" type="data" format="gff3" optional="true" label="Genes in GFF3 format" help="" />
-      </when>
-    </conditional> 
-    <conditional name="dbsnp">
-      <param name="snp_source" type="select" label="Add SNP info from" >
-        <option value="none"></option>
-        <option value="snpTable">UCSC SNP Table</option>
-        <option value="snpFile">GMAP SNP File</option>
-      </param>
-      <when value="none"/>
-      <when value="snpTable">
-        <param name="snps" type="data" format="tabular" optional="true" 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;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>
-    </conditional> 
-  </inputs>
-  <outputs>
-    <!--
-    <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
-    -->
-    <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" />
-  </outputs>
-  <configfiles>
-    <configfile name="shscript">
-#!/bin/bash
-#set $ds = chr(36)
-#set $gt = chr(62)
-#set $lt = chr(60)
-#set $ad = chr(38)
-## #set $ref_files = ''
-## #for $i in $inputs:
-  ## #set $ref_files = $ref_files $i.input
-## #end for
-## echo $ref_files
-#import os.path
-#set $gmapdb = $output.extra_files_path
-#set $mapsdir = $os.path.join($os.path.join($gmapdb,str($refname)), str($refname) + '.maps')
-mkdir -p $gmapdb
-## export GMAPDB required for cmetindex  and atoiindex
-export GMAPDB=$gmapdb
-#for $k in $kmer.__str__.split(','):
-gmap_build -D $gmapdb -d $refname -s numeric-alpha -k $k #for i in $inputs# ${i.input}#end for#
-#end for
-get-genome -D $gmapdb -d '?' | sed 's/^Available .*/gmap db: /' 
-echo "kmers: " $kmer 
-#if $splicesite.splice_source == 'refGeneTable':
-#if $splicesite.refGenes.__str__ != 'None':
-cat $splicesite.refGenes | psl_splicesites -s $splicesite.col_skip | iit_store -o  $os.path.join($mapsdir,'splicesites')
-cat $splicesite.refGenes | psl_introns -s $splicesite.col_skip | iit_store -o  $os.path.join($mapsdir,'introns')
-#end if
-#elif $splicesite.splice_source == 'gtf':
-#if $splicesite.gtfGenes.__str__ != 'None':
-cat $splicesite.gtfGenes | gtf_splicesites | iit_store -o  $os.path.join($mapsdir,'splicesites')
-cat $splicesite.gtfGenes | gtf_introns | iit_store -o  $os.path.join($mapsdir,'introns')
-#end if
-#elif $splicesite.splice_source == 'gff3':
-#if $splicesite.gff3Genes.__str__ != 'None':
-cat $splicesite.gff3Genes | gff3_splicesites | iit_store -o  $os.path.join($mapsdir,'splicesites')
-cat $splicesite.gff3Genes | gff3_introns | iit_store -o  $os.path.join($mapsdir,'introns')
-#end if
-#end if
-#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  $os.path.join($mapsdir,'snps')
-#else:
-cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight | iit_store -o  $os.path.join($mapsdir,'snps')
-#end if
-#else:
-cat $dbsnp.snps | iit_store -o  $os.path.join($mapsdir,'snps')
-#end if
-snpindex -d $refname -v snps
-echo "snpindex" -d  $refname -v snps
-#end if
-#if $cmetindex.__str__ == 'yes':
-cmetindex -d $refname
-echo "cmetindex" -d $refname
-#end if
-#if $atoiindex.__str__ == 'yes':
-atoiindex -d $refname
-echo "atoiindex" -d $refname
-#end if
-get-genome -D $gmapdb -d $refname -m '?' | sed 's/^Available maps .*/maps: /' 
-    </configfile>
-  </configfiles>
-
-  <tests>
-  </tests> 
-
-  <help>
-
-
-**GMAP Build**
-
-GMAP Build creates an index of a genomic sequence for mapping and alignment using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program).  (GMAP Build uses GMSP commands: gmap_build, iit_store, psl_splicesites, psl_introns, gtf_splicesites, gtf_introns, gff3_splicesites, gff3_introns, dbsnp_iit, snpindex, cmetindex, and atoiindex.)
-
-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>
-
diff -r 93911bac43da -r 6adc485b6dc0 gsnap.xml
--- a/gsnap.xml	Thu Jan 05 14:31:24 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,864 +0,0 @@
-<tool id="gsnap" name="GSNAP" version="2.0.1">
-  <description>Genomic Short-read Nucleotide Alignment Program</description>
-  <requirements>
-      <requirement type="binary">gsnap</requirement>
-  </requirements>
-  <version_string>gsnap --version</version_string>
-  <command>
-    #import os.path, re
-    gsnap
-    --nthreads="4" --ordered
-    #if $refGenomeSource.genomeSource == "gmapdb":
-      #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0]
-      --dir=$refGenomeSource.gmapdb.extra_files_path --db=$refGenomeSource.gmapdb.metadata.db_name
-    #else:
-      --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value)
-    #end if
-    #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:
-      --kmer=$refGenomeSource.kmer
-    #end if
-    #if $refGenomeSource.use_splicing.src == 'gmapdb':
-      #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:
-        -s $refGenomeSource.use_splicing.splicemap.value
-        #if $computation.trim_mismatch_score.__str__ == '0':
-          $ambig_splice_noclip
-        #end if
-      #end if
-    #elif $refGenomeSource.use_splicing.src == 'history':
-      #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:
-        -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap)
-        #if $computation.trim_mismatch_score.__str__ == '0':
-          $ambig_splice_noclip
-        #end if
-      #end if
-    #end if
-    #if $refGenomeSource.use_snps.src == 'gmapdb':
-       #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0:
-        -v $refGenomeSource.use_snps.snpindex.value
-       #end if
-    #elif $refGenomeSource.use_snps.src == 'history':
-       #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0:
-         -V $refGenomeSource.use_snps.snpindex.extra_files_path -v $refGenomeSource.use_snps.snpindex.metadata.snps_name
-       #end if
-    #end if
-    #if $refGenomeSource.mode.__str__ != '':
-      --mode=$refGenomeSource.mode
-    #end if
-    #* ## No longer in options as of version 2011-11-30
-    #if $mapq_unique_score.__str__ != '':
-      --mapq-unique-score=$mapq_unique_score
-    #end if
-    *#
-    #if $computation.options == "advanced":
-      #if $computation.max_mismatches.__str__ != '':
-        --max-mismatches=$computation.max_mismatches
-      #end if
-      $computation.query_unk_mismatch
-      $computation.genome_unk_mismatch
-      #if $computation.terminal_threshold.__str__ != '':
-        --terminal-threshold=$computation.terminal_threshold
-      #end if
-      #if $computation.indel_penalty.__str__ != '':
-        --indel-penalty=$computation.indel_penalty
-      #end if
-      #if $computation.indel_endlength.__str__ != '':
-        --indel-endlength=$computation.indel_endlength
-      #end if
-      #if $computation.max_middle_insertions.__str__ != '':
-        --max-middle-insertions=$computation.max_middle_insertions
-      #end if
-      #if $computation.max_middle_deletions.__str__ != '':
-        --max-middle-deletions=$computation.max_middle_deletions
-      #end if
-      #if $computation.max_end_insertions.__str__ != '':
-        --max-end-insertions=$computation.max_end_insertions
-      #end if
-      #if $computation.max_end_deletions.__str__ != '':
-        --max-end-deletions=$computation.max_end_deletions
-      #end if
-      #if $computation.suboptimal_levels.__str__ != '':
-        --suboptimal-levels=$computation.suboptimal_levels
-      #end if
-      #if $computation.adapter_strip.__str__ != '':
-        --adapter-strip=$computation.adapter_strip
-      #end if
-      #if $computation.trim_mismatch_score.__str__ != '':
-        --trim-mismatch-score=$computation.trim_mismatch_score
-      #end if
-      #if $computation.trim_indel_score.__str__ != '':
-        --trim-indel-score=$computation.trim_indel_score
-      #end if
-      ## TODO - do we need these options (Is it tally XOR runlength?):
-      ## --tallydir=  --use-tally=tally
-      ## --runlengthdir  --use-runlength=runlength
-      #if $computation.use_tally != None and len($computation.use_tally.__str__) > 0:
-        ##--tallydir $os.path.dirname($computation.use_tally) --use-tally $os.path.basename($computation.use_tally)
-        --use-tally=$computation.use_tally
-      #end if
-      ## gmap options
-      #if $computation.gmap_mode.__str__ != '' and  $computation.gmap_mode.__str__ != 'None':
-        --gmap-mode='$computation.gmap_mode'
-      #end if
-      #if $computation.trigger_score_for_gmap.__str__ != '':
-        --trigger-score-for-gmap=$computation.trigger_score_for_gmap
-      #end if
-      #if $computation.max_gmap_pairsearch.__str__ != '' and $re.search("pairsearch",$computation.gmap_mode):
-        --max-gmap-pairsearch=$computation.max_gmap_pairsearch
-      #end if
-      #if $computation.max_gmap_terminal.__str__ != '' and $re.search("terminal",$computation.gmap_mode):
-        --max-gmap-terminal=$computation.max_gmap_terminal
-      #end if
-      #if $computation.max_gmap_improvement.__str__ != '' and $re.search("improv",$computation.gmap_mode):
-        --max-gmap-improvement=$computation.max_gmap_improvement
-      #end if
-      #if $computation.microexon_spliceprob.__str__ != '':
-        --microexon-spliceprob=$computation.microexon_spliceprob
-      #end if
-    #end if
-    #if $splicing.options == "advanced":
-      $splicing.novelsplicing
-      #if $splicing.localsplicedist.__str__ != '':
-        --localsplicedist=$splicing.localsplicedist
-      #end if
-      #if $splicing.local_splice_penalty.__str__ != '':
-        --local-splice-penalty=$splicing.local_splice_penalty
-      #end if
-      #if $splicing.distant_splice_penalty.__str__ != '':
-        --distant-splice-penalty=$splicing.distant_splice_penalty
-      #end if
-      #if $splicing.local_splice_endlength.__str__ != '':
-        --local-splice-endlength=$splicing.local_splice_endlength
-      #end if
-      #if $splicing.distant_splice_endlength.__str__ != '':
-        --distant-splice-endlength=$splicing.distant_splice_endlength
-      #end if
-      #if $splicing.distant_splice_identity.__str__ != '':
-        --distant-splice-identity=$splicing.distant_splice_identity
-      #end if
-    #end if
-    #if $output.options == "advanced":
-      #if $output.npath.__str__ != '':
-        --npath=$output.npath
-      #end if
-      $output.quiet_if_excessive
-      $output.show_refdiff
-      $output.clip_overlap
-    #end if
-    #if $result.format == "sam":
-      --format=sam
-      $result.no_sam_headers
-      #if $result.read_group_id.__str__.strip != '':
-         --read-group-id='$result.read_group_id'
-      #end if
-      #if $result.read_group_name.__str__ != '':
-         --read-group-name='$result.read_group_name'
-      #end if
-      #if $result.read_group_library.__str__ != '':
-         --read-group-library='$result.read_group_library'
-      #end if
-      #if $result.read_group_platform.__str__ != '':
-         --read-group-platform='$result.read_group_platform'
-      #end if
-      #if $result.quality_shift.__str__ != '':
-        --quality-shift=$result.quality_shift
-      #end if
-    #elif $result.format == "goby":
-      #if $result.goby_output.__str__ != '':
-        --goby-output='$result.goby_output'
-      #end if
-      #if $result.creads_window_start.__str__ != '':
-        --creads-window-start=$result.creads_window_start
-      #end if
-      #if $result.creads_window_end.__str__ != '':
-        --creads-window-end=$result.creads_window_end
-      #end if
-      $result.creads_complement
-    #end if
-    #if $results.split_output == 'yes':
-      --split-output=gsnap_out
-      #if $results.fails.choice == 'nofails':
-        --nofails
-      #elif $results.fails.choice == 'failsonly':
-        --failsonly
-      #end if
-      $results.fails_as_input
-    #else
-      #if $results.fails.choice == 'nofails':
-        --nofails
-      #elif $results.fails.choice == 'failsonly':
-        --failsonly
-        $results.fails.fails_as_input
-      #end if
-    #end if
-    #if $seq.format == "gsnap_fasta":
-      $seq.circularinput $seq.gsnap
-    #else if $seq.format == "fastq":
-      #if $seq.barcode_length.__str__ != '':
-        --barcode-length=$seq.barcode_length
-      #end if
-      #if $seq.fastq_id_start.__str__ != '':
-        --fastq-id-start=$seq.fastq_id_start
-      #end if
-      #if $seq.fastq_id_end.__str__ != '':
-        --fastq-id-end=$seq.fastq_id_end
-      #end if
-      #if $seq.filter_chastity.__str__ != 'off':
-        --filter-chastity=$seq.filter_chastity
-      #end if
-      #if $seq.paired.ispaired.__str__ == 'yes':
-        #if $seq.paired.pairmax_dna.__str__ != '':
-          --pairmax-dna=$seq.paired.pairmax_dna
-        #end if
-        #if $seq.paired.pairmax_rna.__str__ != '':
-          --pairmax-rna=$seq.paired.pairmax_rna
-        #end if
-        #if $seq.paired.pairexpect.__str__ != '':
-          --pairexpect=$seq.paired.pairexpect
-        #end if
-        #if $seq.paired.pairdev.__str__ != '':
-          --pairdev=$seq.paired.pairdev
-        #end if
-        $seq.fastq $seq.paired.fastq
-      #else
-        $seq.fastq
-      #end if
-    #end if
-    #if $results.split_output == 'yes':
-      2> $gsnap_stderr
-    #else:
-      #if $results.fails.choice.__str__ == 'failsonly' and $results.fails.fails_as_input.__str__ != '':
-        2> $gsnap_stderr > $gsnap_fq
-      #else
-        2> $gsnap_stderr > $gsnap_out
-      #end if
-    #end if
-
-  </command>
-  <inputs>
-    <!-- Input data -->
-    <conditional name="seq">
-      <param name="format" type="select" label="&lt;H2&gt;Input Sequences&lt;/H2&gt;Select the input format" help="">
-        <option value="fastq">Fastq</option>
-        <!--
-        <option value="goby">Goby compact-reads</option>
-        -->
-        <option value="gsnap_fasta">GNSAP fasta</option>
-      </param>
-      <when value="fastq">
-        <param name="fastq" type="data" format="fastq" label="Select a fastq dataset" />
-        <conditional name="paired">
-          <param name="ispaired" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use Paired Reads?"/>
-          <when value="no"/>
-          <when value="yes">
-            <param name="fastq" type="data" format="fastq" label="Select the paired reads reverse dataset" />
-            <param name="orientation" type="select" label="Orientation of paired-end reads" help="">
-              <option value="FR">fwd-rev, typical Illumina default</option>
-              <option value="RF">rev-fwd, for circularized inserts</option>
-              <option value="FF">fwd-fwd, same strand</option>
-            </param>
-            <param name="pairmax_dna"  type="integer" value="" optional="true" label="Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000)." help="Used if no splice file is provided and novelsplicing is off."/>
-            <param name="pairmax_rna"  type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used when novel splicing is specified or a splice file is provided.  Should probably match the value for localsplicedist."/>
-            <param name="pairexpect"  type="integer" value="" optional="true" label="Expected paired-end length" 
-                   help="Used for calling splices in medial part of paired-end reads (default 200)"/>
-            <param name="pairdev"  type="integer" value="" optional="true" label="Allowable deviation from expected paired-end length" 
-                   help="Used for calling splices in medial part of paired-end reads (default 25)"/>
-          </when>
-        </conditional>
-        <param name="barcode_length" type="integer" value="" optional="true"  label="Amount of barcode to remove from start of read (default 0)" />
-        <param name="fastq_id_start" type="integer" value="" optional="true"  label="Starting field  of identifier in FASTQ header, whitespace-delimited, starting from 1" />
-        <param name="fastq_id_end" type="integer" value="" optional="true"  label="Ending field  of identifier in FASTQ header, whitespace-delimited, starting from 1" 
-             help="Examples:
-                  &lt;br&gt;@HWUSI-EAS100R:6:73:941:1973#0/1
-                  &lt;br&gt; . start=1, end=1 (default)  => identifier is HWUSI-EAS100R:6:73:941:1973#0/1
-                  &lt;br&gt;@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
-                  &lt;br&gt; . start=1, end=1  => identifier is SRR001666.1
-                  &lt;br&gt; . start=2, end=2  => identifier is 071112_SLXA-EAS1_s_7:5:1:817:345
-                  &lt;br&gt; . start=1, end=2  => identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345"
-        />
-        <param name="filter_chastity" type="select" label="Skip reads marked by the Illumina chastity program" 
-               help="String after the accession having a  'Y'  after the first colon, like this:  
-                    &lt;br&gt;@accession 1:Y:0:CTTGTA
-                    &lt;br&gt;where the  'Y'  signifies filtering by chastity.
-                    &lt;br&gt; For 'either', a  'Y'  on either end of a paired-end read will be filtered.
-                    &lt;br&gt;  For 'both', a  'Y'  is required on both ends of a paired-end read (or on the only end of a single-end read)"
-          >
-          <option value="off">off - no filtering</option>
-          <option value="either">either - a 'Y' on either end of a paired-end read</option>
-          <option value="both">both - a 'Y' is required on both ends of a paired-end read or the only end of a single-end read</option>
-        </param>
-      </when>
-      <!--
-      <when value="goby">
-      </when>
-      -->
-      <when value="gsnap_fasta">
-        <param name="gsnap" type="data" format="fasta" label="Select a single-end dataset" help="GSNAP fasta must have the sequence entirely on one line, a second line is interpreted as the paired-end sequence"/>
-        <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/>
-      </when>
-      
-    </conditional>
-    <!-- No longer in options as of version 2011-11-30
-    <param name="mapq_unique_score"  type="integer" value="" optional="true" label="MAPQ score threshold" 
-                help="For multiple results, consider as a unique result if only one of the results has a MAPQ score equal or greater than this
-                      (if not selected, then reports all multiple results, up to npaths)" />
-    -->
-
-    <!-- GMAPDB for alignment -->
-    <conditional name="refGenomeSource">
-     <param name="genomeSource" type="select" label="&lt;HR&gt;&lt;H2&gt;Align To&lt;/H2&gt;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="gmapdb">Use a gmapdb from your 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>
-
-        <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size">
-          <options from_file="gmap_indices.loc">
-            <column name="name" index="3"/>
-            <column name="value" index="3"/>
-            <filter type="param_value" ref="gmapindex" column="6"/>
-            <filter type="multiple_splitter" column="3" separator=","/>
-            <filter type="add_value" name="" value=""/>
-            <filter type="sort_by" column="3"/>
-          </options>
-        </param>
-
-        <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase.">
-            <option value="">standard</option>
-            <option value="cmet-stranded">cmet-stranded   for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
-            <option value="cmet-nonstranded">cmet-nonstranded   for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
-            <option value="atoi-stranded">atoi-stranded   for RNA-editing tolerance (A-to-G changes)</option>
-            <option value="atoi-nonstranded">atoi-nonstranded   for RNA-editing tolerance (A-to-G changes)</option>
-        </param>
-
-        <conditional name="use_splicing">
-          <param name="src" type="select" label="&lt;HR&gt;Known Splicesite and Introns" 
-                 help="Look for splicing involving known sites or known introns at short or long distances 
-                  See README instructions for the distinction between known sites and known introns">
-            <option value="none" selected="true">None</option>
-            <option value="gmapdb">From the GMAP Database</option>
-            <option value="history">A Map in your history</option>
-          </param>
-          <when value="none"/>
-          <when value="history">
-            <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map" 
-              help="built with GMAP IIT"/>
-          </when>
-          <when value="gmapdb">
-            <param name="splicemap" type="select" data_ref="gmapindex" label="Use map for splicing involving known sites or known introns" help="">
-              <options from_file="gmap_indices.loc">
-                <column name="name" index="4"/>
-                <column name="value" index="4"/>
-                <filter type="param_value" ref="gmapindex" column="6"/>
-                <filter type="multiple_splitter" column="4" separator=","/>
-                <filter type="add_value" name="" value=""/>
-                <filter type="sort_by" column="4"/>
-              </options>
-            </param>
-          </when>
-        </conditional>
-
-        <conditional name="use_snps">
-          <param name="src" type="select" label="&lt;HR&gt;Known SNPs" help="for SNP tolerant alignments">
-            <option value="none" selected="true">None</option>
-            <option value="gmapdb">From the GMAP Database</option>
-            <option value="history">A SNP Index in your history</option>
-          </param>
-          <when value="none"/>
-          <when value="history">
-            <param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex" 
-              help="built with GMAP SNP Index"/>
-          </when>
-          <when value="gmapdb">
-            <param name="snpindex" type="select" data_ref="gmapindex" label="Use database containing known SNPs" help="">
-              <options from_file="gmap_indices.loc">
-                <column name="name" index="5"/>
-                <column name="value" index="5"/>
-                <filter type="param_value" ref="gmapindex" column="6"/>
-                <filter type="multiple_splitter" column="5" separator=","/>
-                <filter type="add_value" name="" value=""/>
-                <filter type="sort_by" column="5"/>
-              </options>
-            </param>
-          </when>
-        </conditional>
-
-      </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"/>
-        <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size">
-          <options>
-            <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/>
-          </options>
-        </param>
-
-        <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase.">
-            <option value="">standard</option>
-            <option value="cmet-stranded">cmet-stranded   for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
-            <option value="cmet-nonstranded">cmet-nonstranded   for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
-            <option value="atoi-stranded">atoi-stranded   for RNA-editing tolerance (A-to-G changes)</option>
-            <option value="atoi-nonstranded">atoi-nonstranded   for RNA-editing tolerance (A-to-G changes)</option>
-        </param>
-
-        <conditional name="use_splicing">
-          <param name="src" type="select" label="&lt;HR&gt;Known Splicesite and Introns" 
-                 help="Look for splicing involving known sites or known introns at short or long distances 
-                  See README instructions for the distinction between known sites and known introns">
-            <option value="none" selected="true">None</option>
-            <option value="gmapdb">From the GMAP Database</option>
-            <option value="history">A Map in your history</option>
-          </param>
-          <when value="none"/>
-          <when value="history">
-            <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map" 
-              help="built with GMAP IIT"/>
-            <param name="ambig_splice_noclip"  type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites"
-              help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron.  
-                    This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>
-          </when>
-          <when value="gmapdb">
-            <param name="splicemap" type="select"  data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help="">
-              <options>
-                <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/>
-              </options>
-            </param>
-            <param name="ambig_splice_noclip"  type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites"
-              help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron.  
-                    This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>
-          </when>
-        </conditional>
-
-        <conditional name="use_snps">
-          <param name="src" type="select" label="&lt;HR&gt;Known SNPs" help="for SNP tolerant alignments">
-            <option value="none" selected="true">None</option>
-            <option value="gmapdb">From the GMAP Database</option>
-            <option value="history">A SNP Index in your history</option>
-          </param>
-          <when value="none"/>
-          <when value="history">
-            <param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex" 
-              help="built with GMAP SNP Index"/>
-          </when>
-          <when value="gmapdb">
-            <param name="snpindex" type="select"  data_ref="gmapdb" label="Use database containing known SNPs" help="">
-              <options>
-                <filter type="data_meta" ref="gmapdb" key="snps" multiple="True" separator=","/>
-              </options>
-            </param>
-          </when>
-        </conditional>
-
-      </when>
-    </conditional>
-
-    <!-- Computation options -->
-    <conditional name="computation">
-      <param name="options" type="select" label="&lt;HR&gt;Computational Settings" help="">
-        <option value="default">Use default settings</option>
-        <option value="advanced">Set Computation Options</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-         <param name="max_mismatches" type="float" value="" optional="true" label="Maximum number of mismatches allowed (uses default when negative)" 
-              help="Defaults to the ultrafast level of ((readlength+2)/12 - 2)).
-                    If specified between 0.0 and 1.0, then treated as a fraction
-                    of each read length.  Otherwise, treated as an integral number
-                    of mismatches (including indel and splicing penalties)
-                    For RNA-Seq, you may need to increase this value slightly
-                    to align reads extending past the ends of an exon.">
-            <validator type="in_range" message="The mismatches must >= 0." min="0."/>
-         </param>
-         <param name="query_unk_mismatch" type="boolean" checked="false" truevalue="--query-unk-mismatch=1" falsevalue="" label="Count unknown (N) characters in the query as a mismatch"/>
-         <param name="genome_unk_mismatch" type="boolean" checked="true" truevalue="" falsevalue="--genome-unk-mismatch=0" label="Count unknown (N) characters in the genome as a mismatch"/>
-         <param name="terminal_threshold"  type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 2)" 
-                help="(from one end of the read to the best possible position at the other end).   For example, if this value is 2, then if GSNAP finds an exact or
-                                   1-mismatch alignment, it will not try to find a terminal alignment.
-                                   Note that this default value may not be low enough if you want to
-                                   obtain terminal alignments for very short reads, although such reads
-                                   probably don't have enough specificity for terminal alignments anyway." />
-         <param name="indel_penalty"  type="integer" value="" optional="true" label="Penalty for an indel (default 2)" 
-                help="Counts against mismatches allowed.  To find indels, make indel-penalty less than or equal to max-mismatches.  A value &lt; 2 can lead to false positives at read ends" />
-         <param name="indel_endlength"  type="integer" value="" optional="true" label="Minimum length at end required for indel alignments (default 4)" />
-         <param name="max_middle_insertions"  type="integer" value="" optional="true" label="Maximum number of middle insertions allowed (default 9)" />
-         <param name="max_middle_deletions"  type="integer" value="" optional="true" label="Maximum number of middle deletions allowed (default 30)" />
-         <param name="max_end_insertions"  type="integer" value="" optional="true" label="Maximum number of end insertions allowed (default 3)" />
-         <param name="max_end_deletions"  type="integer" value="" optional="true" label="Maximum number of end deletions allowed (default 6)" />
-         <param name="suboptimal_levels"  type="integer" value="" optional="true" label="Report suboptimal hits beyond best hit (default 0)"
-                help="All hits with best score plus suboptimal-levels are reported" />
-         <param name="adapter_strip"  type="select" label="Method for removing adapters from reads" 
-                help="paired removes adapters from paired-end reads if a concordant or paired alignment cannot be found from the original read">
-           <option value="paired" selected="true">paired</option>
-           <option value="off">off</option>
-         </param>
-         <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)" 
-                help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive mismatches at the ends of reads)"/>
-         <param name="trim_indel_score" type="integer" value="" optional="true" label="Score to use for indels when trimming at ends (default is -4)" 
-                help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive indels at the ends of reads)"/>
-         <param name="use_tally" type="data" format="tally.iit" optional="true" metadata_name="dbkey" label="Select a tally IIT file to resolve concordant multiple results" 
-              help="generated by gsnap_tally and iit_store"/>
-
-         <!--
-           tallydir=STRING              Directory for tally IIT file to resolve concordant multiple results (default is
-                                              location of genome index files specified using -D and -d).  Note: can
-                                              just give full path name to use-tally instead.
-           use-tally=STRING             Use this tally IIT file to resolve concordant multiple results
-           runlengthdir=STRING          Directory for runlength IIT file to resolve concordant multiple results (default is
-                                              location of genome index files specified using -D and -d).  Note: can
-                                              just give full path name to use-runlength instead.
-           use-runlength=STRING         Use this runlength IIT file to resolve concordant multiple results
-         -->
-         
-         <!-- Options for GMAP alignment within GSNAP -->
-          <param name="gmap_mode" type="select" multiple="true" optional="true" display="checkboxes" label="Cases to use GMAP for complex alignments containing multiple splices or indels" 
-                 help="Default: pairsearch,terminal,improve">
-            <option value="pairsearch" selected="true">pairsearch</option>
-            <option value="terminal" selected="true">terminal</option>
-            <option value="improve" selected="true">improve</option>
-          </param>
-          <param name="trigger_score_for_gmap" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 5)" 
-                 help="Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5)" />
-          <param name="max_gmap_pairsearch" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 3)" 
-                 help="Perform GMAP pairsearch on nearby genomic regions up to this many candidate ends (default 3)." />
-          <param name="max_gmap_terminal" type="integer" value="" optional="true" label="GMAP terminal threshold (default 3)" 
-                 help="Perform GMAP terminal on nearby genomic regions up to this many candidate ends (default 3)." />
-          <param name="max_gmap_improvement" type="integer" value="" optional="true" label="GMAP improvement threshold (default 3)" 
-                 help="Perform GMAP improvement on nearby genomic regions up to this many candidate ends (default 3)." />
-          <param name="microexon_spliceprob"  type="float" value="" optional="true" label="GMAP microexons threshold (default .90)" 
-                 help="Allow microexons only if one of the splice site probabilities is greater than this value." >
-            <validator type="in_range" message="The microexons  probability must be between 0. and 1." min="0." max="1."/>
-          </param>
-      </when>
-    </conditional>
-
-    <conditional name="splicing">
-      <param name="options" type="select" label="&lt;HR&gt;Splicing options for RNA-Seq" help="">
-        <option value="default">Use default settings</option>
-        <option value="advanced">Set Splicing Options</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-         <!-- Splicing options for RNA-Seq -->
-         <!-- use-splicing This should be either a select list from the gmapdb maps or a data type using splicesdir and use-splicing --> 
-         <!-- Neither novel splicing (-N) nor known splicing (-s) turned on => assume reads are DNA-Seq (genomic) -->
-         <param name="novelsplicing" type="boolean" checked="false" truevalue="--novelsplicing=1" falsevalue="" label="Look for novel splicing "/>
-         <param name="localsplicedist"  type="integer" value="" optional="true" label="Definition of local novel splicing event (default 200000)"/>
-         <param name="local_splice_penalty"  type="integer" value="" optional="true" label="Penalty for a local splice (default 0).  Counts against mismatches allowed"/>
-         <param name="distant_splice_penalty"  type="integer" value="" optional="true" label="Penalty for a distant splice (default 3).  Counts against mismatches allowed"
-                help="A distant splice is one where the intron length exceeds the value of localsplicedist or is an
-                     inversion, scramble, or translocation between two different chromosomes. Counts against mismatches allowed"/>
-         <param name="distant_splice_endlength"  type="integer" value="" optional="true" label="Minimum length at end required for distant spliced alignments"
-                help="(default 16, min is the kmer length)"/>
-         <param name="shortend_splice_endlength"  type="integer" value="" optional="true" label="Minimum length at end required for short-end spliced alignments"
-                help="(default 2, but unless known splice sites are provided,  GSNAP may still need the end length to be the value of kmer size to find a given splice"/>
-         <param name="distant_splice_identity"  type="float" value="" optional="true" label="Minimum identity at end required for distant spliced alignments (default 0.95)"/>
-         <param name="antistranded_penalty"  type="integer" value="" optional="true" label="Penalty for antistranded splicing when using stranded RNA-Seq protocols" 
-                help="A positive value, such as 1, expects antisense on the first read and sense on the second read.  
-                      Default is 0, which treats sense and antisense equally well"/>
-      </when>
-    </conditional>
-
-    <!-- Output data -->
-    <conditional name="output">
-      <param name="options" type="select" label="&lt;HR&gt;&lt;H2&gt;Output&lt;/H2&gt;Output options for RNA-Seq" help="">
-        <option value="default">Use default settings</option>
-        <option value="advanced">Set Output Options</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-        <param name="npath"  type="integer" value="" optional="true" label="Maximum number of paths to print (default 100)"/>
-        <param name="quiet_if_excessive" type="boolean" checked="false" truevalue="--quiet-if-excessive" falsevalue="" label="Quiet if Excessive" 
-               help="If more than maximum number of paths are found, then nothing is printed."/>
-        <param name="show_refdiff" type="boolean" checked="false" truevalue="--show-refdiff" falsevalue="" label="Show SNP-tolerant alignment" 
-               help="For GSNAP output in SNP-tolerant alignment, shows all differences relative to the reference genome as lower case (otherwise, it shows all differences relative to both the reference and alternate genome)"/>
-        <param name="clip_overlap" type="boolean" checked="false" truevalue="--clip-overlap" falsevalue="" label="Clip Overlap" 
-               help="For paired-end reads whose alignments overlap, clip the overlapping region."/>
-      </when>
-    </conditional>
-    <conditional name="result">
-      <param name="format" type="select" label="Select the output format" help="">
-        <option value="sam">SAM</option>
-        <!--  goby should only be an option if the input is in goby format
-        <option value="goby">Goby</option>
-        -->
-        <option value="gsnap">GSNAP default output</option>
-      </param>
-      <when value="gsnap">
-      </when>
-      <when value="sam">
-        <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/>
-        <param name="read_group_id" type="text" value="" optional="true" label="Value to put into read-group id (RG-ID) field"/>
-        <param name="read_group_name" type="text" value="" optional="true" label="Value to put into read-group name (RG-SM) field"/>
-        <param name="read_group_library" type="text" value="" optional="true" label="Value to put into read-group library (RG-LB) field"/>
-        <param name="read_group_platform" type="text" value="" optional="true" label="Value to put into read-group library platform (RG-PL) field"/>
-        <param name="quality_shift"  type="integer" value="" optional="true" label="Shift FASTQ quality scores by this amount in SAM output (default -31)"/>
-      </when>
-      <!--
-      <when value="goby">
-        <param name="goby_output" type="text" value="" label="Basename for Goby output files"/>
-        <param name="creads_window_start"  type="integer" value="" optional="true" label="Compact reads window start (default: 0=start of file)"/>
-        <param name="creads_window_end"  type="integer" value="" optional="true" label="Compact reads window end (default: 0=end of file)"/>
-        <param name="creads_complement" type="boolean" truevalue="-\-creads-complement" falsevalue="" checked="false" label="Complement read sequences (without reversing)"/>
-      </when>
-      -->
-    </conditional>
-    <!-- TODO combine fails and split_output -->
-
-    <conditional name="results">
-      <param name="split_output" type="select" label="&lt;HR&gt;Split outputs" 
-       help="Separate outputs for: nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult results"> 
-        <option value="no">no</option>
-        <option value="yes">yes</option>
-      </param>
-      <when value="no">
-        <conditional name="fails">
-          <param name="choice" type="select" label="How to deal with fails" help="">
-            <option value="default">default - include them in results</option>
-            <option value="nofails">nofails - exclude fails from results</option>
-            <option value="failsonly">failsonly - only output failing results</option>
-          </param>
-          <when value="default"/>
-          <when value="nofails"/>
-          <when value="failsonly">
-            <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format" 
-              help=""/> 
-          </when>
-        </conditional>
-      </when>
-      <when value="yes">
-        <conditional name="fails">
-          <param name="choice" type="select" label="How to deal with fails" help="">
-            <option value="default">default - include them in results</option>
-            <option value="nofails">nofails - exclude fails from results</option>
-            <option value="failsonly">failsonly - only output failing results</option>
-          </param>
-          <when value="default"/>
-          <when value="nofails"/>
-          <when value="failsonly"/>
-        </conditional>
-        <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format" 
-              help=""/> 
-      </when>
-    </conditional>
-
-  </inputs>
-  <outputs>
-    <data format="txt" name="gsnap_stderr" label="${tool.name} on ${on_string}: gsnap.log"/>
-
-    <data format="txt" name="gsnap_out" label="${tool.name} on ${on_string} ${result.format}" >
-      <filter>(results['split_output'] == 'no' and (results['fails']['choice'] != 'failsonly' or results['fails']['fails_as_input'] == False))</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-
-    <data format="fastq" name="gsnap_fq" label="${tool.name} on ${on_string} fails.fq" >
-      <filter>(results['split_output'] == 'no' and results['fails']['choice'] == 'failsonly' and results['fails']['fails_as_input'] == True)</filter>
-    </data>
-
-    <!-- nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, concordant_mult -->
-
-    <data format="txt" name="unpaired_mult" label="${tool.name} on ${on_string} unpaired_mult.${result.format}"  from_work_dir="gsnap_out.unpaired_mult">
-      <filter>(results['split_output'] == 'yes')</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="unpaired_uniq" label="${tool.name} on ${on_string} unpaired_uniq.${result.format}"  from_work_dir="gsnap_out.unpaired_uniq">
-      <filter>(results['split_output'] == 'yes')</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="unpaired_transloc" label="${tool.name} on ${on_string} unpaired_transloc.${result.format}"  from_work_dir="gsnap_out.unpaired_transloc">
-      <filter>(results['split_output'] == 'yes')</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="halfmapping_mult" label="${tool.name} on ${on_string} halfmapping_mult.${result.format}"  from_work_dir="gsnap_out.halfmapping_mult">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="halfmapping_uniq" label="${tool.name} on ${on_string} halfmapping_uniq.${result.format}"  from_work_dir="gsnap_out.halfmapping_uniq">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="halfmapping_transloc" label="${tool.name} on ${on_string} halfmapping_transloc.${result.format}"  from_work_dir="gsnap_out.halfmapping_transloc">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="paired_mult" label="${tool.name} on ${on_string} paired_mult.${result.format}"  from_work_dir="gsnap_out.paired_mult">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="paired_uniq" label="${tool.name} on ${on_string} paired_uniq.${result.format}"  from_work_dir="gsnap_out.paired_uniq">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="paired_transloc" label="${tool.name} on ${on_string} paired_transloc.${result.format}"  from_work_dir="gsnap_out.paired_transloc">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-
-    <data format="txt" name="concordant_mult" label="${tool.name} on ${on_string} concordant_mult.${result.format}"  from_work_dir="gsnap_out.concordant_mult">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="concordant_uniq" label="${tool.name} on ${on_string} concordant_uniq.${result.format}"  from_work_dir="gsnap_out.concordant_uniq">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-    <data format="txt" name="concordant_transloc" label="${tool.name} on ${on_string} concordant_transloc.${result.format}"  from_work_dir="gsnap_out.concordant_transloc">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-
-    <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}"  from_work_dir="gsnap_out.nomapping">
-      <filter>(results['split_output'] == 'yes' and results['fails_as_input'] == False)</filter>
-      <change_format>
-        <when input="result['format']" value="sam" format="sam"/>
-        <when input="result['format']" value="gsnap" format="gsnap"/>
-      </change_format>
-    </data>
-
-    <data format="fastq" name="nomapping_fq" label="${tool.name} on ${on_string} nomapping.fq"  from_work_dir="gsnap_out.nomapping.fq">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == False)</filter>
-    </data>
-
-    <data format="fastq" name="nomapping_1_fq" label="${tool.name} on ${on_string} nomapping.1.fq"  from_work_dir="gsnap_out.nomapping.1.fq">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-    </data>
-
-    <data format="fastq" name="nomapping_2_fq" label="${tool.name} on ${on_string} nomapping.2.fq"  from_work_dir="gsnap_out.nomapping.2.fq">
-      <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
-    </data>
-
-    <!-- Will problay need wrapper code to generate composite datatype for goby alignment
-    <data format="gobyalignment" name="goby_alignment" label="${tool.name} on ${on_string} uniq.${result.format}"  from_work_dir="gsnap_out.nomapping">
-      <filter>result['format'] == 'goby'</filter>
-    </data>
-    -->
-
-  </outputs>
-  <tests>
-  </tests> 
-
-  <help>
-
-**What it does**
-
-GSNAP_ (Genomic Short-read Nucleotide Alignment Program) is a short read aligner which can align both single- and paired-end reads as short as 14nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state. It is developed by Thomas D. Wu of Genentech, Inc.  
-Publication_ citation: Thomas D. Wu, Serban Nacu "Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010 Apr 1;26(7):873-81. Epub 2010 Feb 10.
-
-.. _GSNAP: http://research-pub.gene.com/gmap/
-.. _Publication: http://bioinformatics.oupjournals.org/cgi/content/full/26/7/873
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844994/?tool=pubmed
-
-------
-
-**Know what you are doing**
-
-.. class:: warningmark
-
-You will want to read the README_
-
-.. _README: http://research-pub.gene.com/gmap/src/README
-
-------
-
-**Input formats**
-
-Input to GSNAP should be either in FASTQ or FASTA format.  
-
-The FASTQ input may include quality scores, which will then be included in SAM
-output, if that output format is selected. 
-
-For FASTA format, you should include one line per read (or end of a
-paired-end read).  The same FASTA file can have a mixture of
-single-end and paired-end reads of varying lengths, if desired.
-
-Single-end reads:
-
-Each FASTA entry should contain one short read per line, like this
-
->Header information
-AAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTA
-
-Each short read can have a different length.  However, the entire read
-needs to be on a single line, and may not wrap around multiple lines.
-If it extends to a second line, GSNAP will think that the read is
-paired-end.
-
-
-Paired-end reads:
-
-Each FASTA entry should contain two short reads, one per line, like
-this
-
->Header information
-AAAACATTCTCCTCCGCATAAGCCTAGTAGATTA
-GGCGTAGGTAGAAGTAGAGGTTAAGGCGCGTCAG
-
-By default, the program assumes that the second end is in the reverse
-complement direction compared with the first end.  If they are in the
-same direction, you may need to use the --circular-input (or -c) flag.
-
-( The Galaxy tool: "FASTA Width formatter"  can be used to reformat fasta files to have single line sequences. )
-
-------
-
-**Output formats in GSNAP**
-
-SAM output format
-
-Default GSNAP format
-  See the README_
-
-
-
-
-  </help>
-</tool>
-
diff -r 93911bac43da -r 6adc485b6dc0 iit_store.xml
--- a/iit_store.xml	Thu Jan 05 14:31:24 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,181 +0,0 @@
-<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>
-  </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>
-
diff -r 93911bac43da -r 6adc485b6dc0 lib/galaxy/datatypes/gmap.py
--- a/lib/galaxy/datatypes/gmap.py	Thu Jan 05 14:31:24 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,472 +0,0 @@
-"""
-GMAP indexes
-"""
-import logging
-import os,os.path,re
-import galaxy.datatypes.data
-from galaxy.datatypes.data import Text
-from galaxy import util
-from galaxy.datatypes.metadata import MetadataElement
-
-log = logging.getLogger(__name__)
-
-class GmapDB( Text ):
-    """
-    A GMAP DB for indexes
-    """
-    MetadataElement( name="db_name", desc="The db name for this index set", default='unknown', set_in_upload=True, readonly=True )
-    MetadataElement( name="basesize", default="12", desc="The basesize for offsetscomp", visible=True, readonly=True )
-    MetadataElement( name="kmers", default=[''], desc="The kmer sizes for indexes", visible=True, no_value=[''], readonly=True )
-    MetadataElement( name="map_dir", desc="The maps directory", default='unknown', set_in_upload=True, readonly=True )
-    MetadataElement( name="maps", default=[''], desc="The names of maps stored for this gmap gmapdb", visible=True, no_value=[''], readonly=True )
-    MetadataElement( name="snps", default=[''], desc="The names of SNP indexes stored for this gmapdb", visible=True, no_value=[''], readonly=True )
-    MetadataElement( name="cmet", default=False, desc="Has a cmet index", visible=True, readonly=True )
-    MetadataElement( name="atoi", default=False, desc="Has a atoi index", visible=True, readonly=True )
-    
-    file_ext = 'gmapdb'
-    is_binary = True
-    composite_type = 'auto_primary_file'
-    allow_datatype_change = False
-
-    def generate_primary_file( self, dataset = None ):
-        """ 
-        This is called only at upload to write the html file
-        cannot rename the datasets here - they come with the default unfortunately
-        """
-        return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
-    
-    def regenerate_primary_file(self,dataset):
-        """
-        cannot do this until we are setting metadata 
-        """
-        bn = dataset.metadata.db_name
-        log.info( "GmapDB regenerate_primary_file %s" % (bn))
-        rval = ['<html><head><title>GMAPDB %s</title></head><p/><H3>GMAPDB %s</H3><p/>cmet %s<br>atoi %s<H4>Maps:</H4><ul>' % (bn,bn,dataset.metadata.cmet,dataset.metadata.atoi)]
-        for i,name in enumerate(dataset.metadata.maps):
-            rval.append( '<li>%s' % name)
-        rval.append( '</ul></html>' )
-        f = file(dataset.file_name,'w')
-        f.write("\n".join( rval ))
-        f.write('\n')
-        f.close()
-
-    def set_peek( self, dataset, is_multi_byte=False ):
-        log.info( "GmapDB set_peek %s" % (dataset))
-        if not dataset.dataset.purged:
-            dataset.peek  = "GMAPDB index %s\n cmet %s\n atoi %s\n maps %s" % ( dataset.metadata.db_name,dataset.metadata.cmet,dataset.metadata.atoi,dataset.metadata.maps )
-            dataset.blurb = "GMAPDB %s" % ( dataset.metadata.db_name )
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-    def display_peek( self, dataset ):
-        try:
-            return dataset.peek
-        except:
-            return "GMAP index file"
-
-    def sniff( self, filename ):
-        return False
-    def set_meta( self, dataset, overwrite = True, **kwd ):
-        """
-        Expecting:
-        extra_files_path/<db_name>/db_name>.ref<basesize><kmer>3<index>
-        extra_files_path/db_name/db_name.ref1[2345]1[2345]3offsetscomp
-        extra_files_path/db_name/db_name.ref1[2345]1[2345]3positions
-        extra_files_path/db_name/db_name.ref1[2345]1[2345]3gammaptrs
-        index maps: 
-        extra_files_path/db_name/db_name.maps/*.iit
-        """
-        log.info( "GmapDB set_meta %s %s" % (dataset,dataset.extra_files_path))
-        pat = '(.*)\.((ref)|(met)[atgc][atgc]|(a2i)[atgc][atgc])((\d\d)(\d\d))?3positions(\.(.+))?'
-        efp = dataset.extra_files_path
-        flist = os.listdir(efp)
-        for i,fname in enumerate(flist):
-            log.info( "GmapDB set_meta %s %s" % (i,fname))
-            fpath = os.path.join(efp,fname)
-            if os.path.isdir(fpath):
-                ilist = os.listdir(fpath)
-                kmers = {'':'default'} # HACK  '' empty key  added so user has default choice when selecting kmer from metadata
-                for j,iname in enumerate(ilist):
-                    log.info( "GmapDB set_meta file %s %s" % (j,iname))
-                    ipath = os.path.join(fpath,iname)
-                    if os.path.isdir(ipath):  # find maps
-                        dataset.metadata.map_dir = iname
-                        for mapfile in os.listdir(ipath):
-                            mapname = mapfile.replace('.iit','')
-                            log.info( "GmapDB set_meta map %s %s" % (mapname,mapfile))
-                            dataset.metadata.maps.append(mapname)
-                    else: 
-                        m = re.match(pat,iname)
-                        if m:
-                            log.info( "GmapDB set_meta m %s %s " % (iname, m))
-                            assert len(m.groups()) == 10
-                            dataset.metadata.db_name = fname
-                            if m.groups()[2] == 'ref':
-                                if m.groups()[-1] != None:
-                                    dataset.metadata.snps.append(m.groups()[-1])
-                                else:
-                                    if m.groups()[-3] != None:
-                                        k = int(m.groups()[-3])
-                                        kmers[k] = k
-                                    if m.groups()[-4] != None:
-                                        dataset.metadata.basesize = int( m.groups()[-4])
-                            elif m.groups()[3] == 'met':
-                                dataset.metadata.cmet = True
-                            elif m.groups()[4] == 'a2i':
-                                dataset.metadata.atoi = True
-                dataset.metadata.kmers = kmers.keys()
-
-class GmapSnpIndex( Text ):
-    """
-    A GMAP SNP index created by snpindex
-    """
-    MetadataElement( name="db_name", desc="The db name for this index set", default='unknown', set_in_upload=True, readonly=True )
-    MetadataElement( name="snps_name", default='snps', desc="The name of SNP index", visible=True, no_value='', readonly=True )
-    
-    file_ext = 'gmapsnpindex'
-    is_binary = True
-    composite_type = 'auto_primary_file'
-    allow_datatype_change = False
-
-    def generate_primary_file( self, dataset = None ):
-        """ 
-        This is called only at upload to write the html file
-        cannot rename the datasets here - they come with the default unfortunately
-        """
-        return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
-    
-    def regenerate_primary_file(self,dataset):
-        """
-        cannot do this until we are setting metadata 
-        """
-        bn = dataset.metadata.db_name
-        log.info( "GmapDB regenerate_primary_file %s" % (bn))
-        rval = ['<html><head><title>GMAPDB %s</title></head><p/><H3>GMAPDB %s</H3><p/>cmet %s<br>atoi %s<H4>Maps:</H4><ul>' % (bn,bn,dataset.metadata.cmet,dataset.metadata.atoi)]
-        for i,name in enumerate(dataset.metadata.maps):
-            rval.append( '<li>%s' % name)
-        rval.append( '</ul></html>' )
-        f = file(dataset.file_name,'w')
-        f.write("\n".join( rval ))
-        f.write('\n')
-        f.close()
-    def set_peek( self, dataset, is_multi_byte=False ):
-        log.info( "GmapSnpIndex set_peek %s" % (dataset))
-        if not dataset.dataset.purged:
-            dataset.peek  = "GMAP SNPindex %s on %s\n" % ( dataset.metadata.snps_name,dataset.metadata.db_name)
-            dataset.blurb = "GMAP SNPindex %s on %s\n" % ( dataset.metadata.snps_name,dataset.metadata.db_name)
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-    def display_peek( self, dataset ):
-        try:
-            return dataset.peek
-        except:
-            return "GMAP SNP index"
-
-    def sniff( self, filename ):
-        return False
-    def set_meta( self, dataset, overwrite = True, **kwd ):
-        """
-        Expecting:
-        extra_files_path/snp_name.iit
-        extra_files_path/db_name/db_name.ref1[2345]1[2345]3offsetscomp.snp_name
-        extra_files_path/db_name/db_name.ref1[2345]1[2345]3positions.snp_name
-        extra_files_path/db_name/db_name.ref1[2345]1[2345]3gammaptrs.snp_name
-        """
-        log.info( "GmapSnpIndex set_meta %s %s" % (dataset,dataset.extra_files_path))
-        pat = '(.*)\.(ref((\d\d)(\d\d))?3positions)\.(.+)?'
-        efp = dataset.extra_files_path
-        flist = os.listdir(efp)
-        for i,fname in enumerate(flist):
-            m = re.match(pat,fname)
-            if m:
-                assert len(m.groups()) == 6
-                dataset.metadata.db_name = m.groups()[0]
-                dataset.metadata.snps_name = m.groups()[-1]
-
-
-
-
-class IntervalIndexTree( Text ):
-    """
-    A GMAP Interval Index Tree Map
-    created by iit_store
-    (/path/to/map)/(mapname).iit
-    """
-    file_ext = 'iit'
-    is_binary = True
-
-class SpliceSitesIntervalIndexTree( IntervalIndexTree ):
-    """
-    A GMAP Interval Index Tree Map 
-    created by iit_store
-    """
-    file_ext = 'splicesites.iit'
-
-class IntronsIntervalIndexTree( IntervalIndexTree ):
-    """
-    A GMAP Interval Index Tree Map
-    created by iit_store
-    """
-    file_ext = 'introns.iit'
-
-class SNPsIntervalIndexTree( IntervalIndexTree ):
-    """
-    A GMAP Interval Index Tree Map
-    created by iit_store
-    """
-    file_ext = 'snps.iit'
-
-class TallyIntervalIndexTree( IntervalIndexTree ):
-    """
-    A GMAP Interval Index Tree Map
-    created by iit_store
-    """
-    file_ext = 'tally.iit'
-
-class IntervalAnnotation( Text ):
-    """
-    Class describing a GMAP Interval format:
-        >label coords optional_tag
-        optional_annotation (which may be zero, one, or multiple lines)
-    The coords should be of the form:
-        chr:position
-        chr:startposition..endposition
-    """
-    file_ext = 'gmap_annotation'
-    """Add metadata elements"""
-    MetadataElement( name="annotations", default=0, desc="Number of interval annotations", readonly=True, optional=True, visible=False, no_value=0 )
-
-    def set_meta( self, dataset, **kwd ):
-        """
-        Set the number of annotations and the number of data lines in dataset.
-        """
-        data_lines = 0
-        annotations = 0
-        for line in file( dataset.file_name ):
-            line = line.strip()
-            if line and line.startswith( '>' ):
-                annotations += 1
-                data_lines +=1
-            else:
-                data_lines += 1
-        dataset.metadata.data_lines = data_lines
-        dataset.metadata.annotations = annotations
-    def set_peek( self, dataset, is_multi_byte=False ):
-        if not dataset.dataset.purged:
-            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-            if dataset.metadata.annotations:
-                dataset.blurb = "%s annotations" % util.commaify( str( dataset.metadata.annotations ) )
-            else:
-                dataset.blurb = data.nice_size( dataset.get_size() )
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-
-    def sniff( self, filename ):
-        """
-        Determines whether the file is a gmap annotation file
-        Format: 
-            >label coords optional_tag
-            optional_annotation (which may be zero, one, or multiple lines)
-        For example, the label may be an EST accession, with the coords
-        representing its genomic position.  Labels may be duplicated if
-        necessary.
-        The coords should be of the form
-            chr:position
-            chr:startposition..endposition
-        The term "chr:position" is equivalent to "chr:position..position".  If
-        you want to indicate that the interval is on the minus strand or
-        reverse direction, then <endposition> may be less than <startposition>.
-        """
-        try:
-            pat = '>(\S+)\s((\S+):(\d+)(\.\.(\d+))?(\s.(.+))?$' #>label chr:position[..endposition][ optional_tag] 
-            fh = open( filename )
-            count = 0
-            while True and count < 10:
-                line = fh.readline()
-                if not line:
-                    break #EOF
-                line = line.strip()
-                if line: #first non-empty line
-                    if line.startswith( '>' ):
-                        count += 1
-                        if re.match(pat,line) == None: # Failed to match 
-                            return False
-        finally:
-            fh.close()
-        return False
-
-class SpliceSiteAnnotation(IntervalAnnotation):
-    file_ext = 'gmap_splicesites'
-    """
-    Example:
-        >NM_004448.ERBB2.exon1 17:35110090..35110091 donor 6678
-        >NM_004448.ERBB2.exon2 17:35116768..35116769 acceptor 6678
-        >NM_004448.ERBB2.exon2 17:35116920..35116921 donor 1179
-        >NM_004448.ERBB2.exon3 17:35118099..35118100 acceptor 1179
-        >NM_004449.ERG.exon1 21:38955452..38955451 donor 783
-        >NM_004449.ERG.exon2 21:38878740..38878739 acceptor 783
-        >NM_004449.ERG.exon2 21:38878638..38878637 donor 360
-        >NM_004449.ERG.exon3 21:38869542..38869541 acceptor 360
-    Each line must start with a ">" character, then be followed by an
-    identifier, which may have duplicates and can have any format, with
-    the gene name or exon number shown here only as a suggestion.  Then
-    there should be the chromosomal coordinates which straddle the
-    exon-intron boundary, so one coordinate is on the exon and one is on
-    the intron.  (Coordinates are all 1-based, so the first character of a
-    chromosome is number 1.)  Finally, there should be the splice type:
-    "donor" or "acceptor".  You may optionally store the intron distance
-    at the end.  GSNAP can use this intron distance, if it is longer than
-    its value for --localsplicedist, to look for long introns at that
-    splice site.  The same splice site may have different intron distances
-    in the database; GSNAP will use the longest intron distance reported
-    in searching for long introns.
-    """
-    def sniff( self, filename ): # TODO
-        """
-        Determines whether the file is a gmap splice site annotation file
-        """
-        try:
-            pat = '>(\S+\.intron\d+)\s((\S+):(\d+)\.\.(\d+))\s(donor|acceptor)(\s(\d+))?$' #>label chr:position..position  donor|acceptor[ intron_dist]
-            fh = open( filename )
-            count = 0
-            while True and count < 10:
-                line = fh.readline()
-                if not line:
-                    break #EOF
-                line = line.strip()
-                if line: #first non-empty line
-                    count += 1
-                    if re.match(pat,line) == None: # Failed to match 
-                        return False
-        finally:
-            fh.close()
-        return False
-
-class IntronAnnotation(IntervalAnnotation):
-    file_ext = 'gmap_introns'
-    """
-    Example:
-        >NM_004448.ERBB2.intron1 17:35110090..35116769
-        >NM_004448.ERBB2.intron2 17:35116920..35118100
-        >NM_004449.ERG.intron1 21:38955452..38878739
-        >NM_004449.ERG.intron2 21:38878638..38869541
-     The coordinates are 1-based, and specify the exon coordinates
-     surrounding the intron, with the first coordinate being from the donor
-     exon and the second one being from the acceptor exon.
-    """
-    def sniff( self, filename ): # TODO
-        """
-        Determines whether the file is a gmap Intron annotation file
-        """
-        try:
-            pat = '>(\S+\.intron\d+)\s((\S+):(\d+)\.\.(\d+)(\s(.)+)?$' #>label chr:position
-            fh = open( filename )
-            count = 0
-            while True and count < 10:
-                line = fh.readline()
-                if not line:
-                    break #EOF
-                line = line.strip()
-                if line: #first non-empty line
-                    count += 1
-                    if re.match(pat,line) == None: # Failed to match 
-                        return False
-        finally:
-            fh.close()
-        return False
-
-class SNPAnnotation(IntervalAnnotation):
-    file_ext = 'gmap_snps'
-    """
-    Example:
-        >rs62211261 21:14379270 CG
-        >rs62211262 21:14379281 AT
-        >rs62211263 21:14379298 WN
-    Each line must start with a ">" 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.  (Previous versions required that
-    these be in alphabetical order: "AC", "AG", "AT", "CG", "CT", or "GT",
-    but that is no longer a requirement.)  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.
-    
-    GSNAP also supports the idea of a wildcard SNP.  A wildcard SNP allows
-    all nucleotides to match at that position, not just a given reference
-    and alternate allele.  It is essentially as if an "N" were recorded at
-    that genomic location, although the index files still keep track of
-    the reference allele.  To indicate that a position has a wildcard SNP,
-    you can indicate the genotype as "WN", where "W" is the reference
-    allele.  Another indication of a wildcard SNP is to provide two
-    separate lines at that position with the genotypes "WX" and "WY",
-    where "W" is the reference allele and "X" and "Y" are two different
-    alternate alleles.
-    """
-    def sniff( self, filename ):
-        """
-        Determines whether the file is a gmap SNP annotation file
-        """
-        try:
-            pat = '>(\S+)\s((\S+):(\d+)\s([TACGW][TACGN])$' #>label chr:position ATCG 
-            fh = open( filename )
-            count = 0
-            while True and count < 10:
-                line = fh.readline()
-                if not line:
-                    break #EOF
-                line = line.strip()
-                if line: #first non-empty line
-                    count += 1
-                    if re.match(pat,line) == None: # Failed to match 
-                        return False
-        finally:
-            fh.close()
-        return False
-
-
-class TallyAnnotation(IntervalAnnotation):
-    file_ext = 'gsnap_tally'
-    """
-    Output produced by gsnap_tally
-    Example:
-        >144 chr20:57268791..57268935
-        G0
-        A1(1@7|1Q-3)
-        A2(1@36,1@1|1Q2,1Q-8)
-        C2      0.889,0.912,0.889,0.889,0.933,0.912,0.912,0.889,0.889,0.889     -2.66,-2.89,-2.66,-2.66,-3.16,-2.89,-2.89,-2.66,-2.66,-2.66
-        C1 T1   0.888,0.9,0.888,0.9,0.913,0.9,0.911,0.888,0.9,0.913     -2.66,-2.78,-2.66,-2.78,-2.91,-2.78,-2.89,-2.66,-2.78,-2.91
-    """
-    def sniff( self, filename ): # TODO
-        """
-        Determines whether the file is a gmap splice site annotation file
-        """
-        try:
-            pat = '^>(\d+)\s((\S+):(\d+)\.\.(\d+))$' #>total chr:position..position
-            pat2 = '^[GATCN]\d.*$' #BaseCountDeatails
-            fh = open( filename )
-            count = 0
-            while True and count < 10:
-                line = fh.readline()
-                if not line:
-                    break #EOF
-                line = line.strip()
-                if line: #first non-empty line
-                    count += 1
-                    if re.match(pat,line) == None and re.match(pat2,line) == None: # Failed to match 
-                        return False
-        finally:
-            fh.close()
-        return False
-
-class GsnapResult( Text ):
-    """
-    The default output format for gsnap.   Can be used as input for gsnap_tally.
-    """
-    file_ext = 'gsnap'
-
-
diff -r 93911bac43da -r 6adc485b6dc0 snpindex.xml
--- a/snpindex.xml	Thu Jan 05 14:31:24 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,136 +0,0 @@
-<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>
-  </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>
-
diff -r 93911bac43da -r 6adc485b6dc0 tool-data/datatypes_conf.xml
--- a/tool-data/datatypes_conf.xml	Thu Jan 05 14:31:24 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-    <datatype_files>
-        <datatype_file name="gmap.py"/>
-    </datatype_files>
-    <registration>
-        <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/>
-        <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/>
-        <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/>
-        <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/>
-        <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/>
-        <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/>
-        <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/>
-        <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/>
-        <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/>
-        <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/>
-    </registration>
-    <sniffers>
-        <sniffer type="galaxy.datatypes.gmap:IntervalAnnotation"/>
-        <sniffer type="galaxy.datatypes.gmap:SpliceSiteAnnotation"/>
-        <sniffer type="galaxy.datatypes.gmap:IntronAnnotation"/>
-        <sniffer type="galaxy.datatypes.gmap:SNPAnnotation"/>
-    </sniffers>
-</datatypes>
diff -r 93911bac43da -r 6adc485b6dc0 tool-data/gmap_indices.loc.sample
--- a/tool-data/gmap_indices.loc.sample	Thu Jan 05 14:31:24 2012 -0600
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of GMAPDB indexed sequences data files.  You will need
-#to create these data files using gmap_build and then create a gmap_indices.loc file 
-#similar to this one (store it in this directory) that points to 
-#the directories in which those files are stored. The gmap_indices.loc 
-#file has this format (white space characters are TAB characters):
-#
-#<unique_build_id>   <dbkey>   <display_name>   <kmers> <map,map>       <snp,snp>       <file_base_path>
-#hg18   hg18    hg18 (cmet atoi)        12,13,14,15     splicesites,introns     snps    /depot/data2/galaxy/gmap/hg18
-#hg19	hg19	hg19 (cmet atoi)	12,13,14,15	splicesites,introns,snps	snps,dbsnp	/depot/data2/galaxy/gmap/hg19
diff -r 93911bac43da -r 6adc485b6dc0 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jul 31 08:19:46 2012 -0400
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="gmap" version="0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2011-11-30.tar.gz</action>
+                <action type="shell_command"> ./configure --prefix=bin --with-gmapdb=../gmapdb</action>
+                <action type="shell_command">make</action>
+                <action type="move_directory_files">
+                    <source_directory>bin</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>