--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gotohscan.xml	Thu Jul 02 12:06:30 2015 -0400
@@ -0,0 +1,103 @@
+<tool id="rbc_gotohscan" name="GotohScan" version="1.3.0">
+    <description>Find subsequences in db</description>
+    <requirements>
+        <requirement type="package" version="1.3">gotohscan</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"  level="fatal" description="Error occurred. Please check Tool Standard Error"/>
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
+    </stdio>
+    <version_command><![CDATA[GotohScan --version | sed -n -e 2p]]></version_command>
+    <command><![CDATA[
+        GotohScan
+        
+        -d $dbase
+        -q $query
+        
+        #if $split and $split is not None
+            --split $split
+        #end if
+        
+        #if $e and $e is not None
+            -e $e
+        #end if
+        
+        #if $p and $p is not None
+            -p $p
+        #end if
+        
+        $s
+        -o $o
+        > 
+        
+        #if $o.value == '0'
+            $output0
+        #elif $o.value == '1'
+            $output1
+        #elif $o.value == '2'
+            $output2
+        #elif $o.value == '3'
+            $output3
+        #elif $o.value == '4'
+            $output4
+        #elif $o.value == '5'
+            $output5
+        #end if
+    ]]></command>
+    <inputs>
+        <param argument="-d" name="dbase" type="data" format="fasta" label="Input Database"/>
+        <param argument="-q" name="query" type="data" format="fasta" label="Input Query"/>
+        <param argument="--split" name="split" type="integer" optional="true" label="Database is split into subsequences of size:" help="default: 10000"/>
+        <param argument="-e" name="e" type="float" optional="true" label="E-value" help="Value should be &lt; 10. default: 1e-3"/>
+        <param argument="-p" name="p" type="float" optional="true" label="Percent identity of aligned sequences" help="Value should be in [0.0,100.00]"/>
+        <param argument="-s" name="s" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Print score distribution data for each query to a file"/>
+        <param argument="-o" name="o" type="select" label="Output Format">
+            <option value="0" selected="true">Blast tabular output</option>
+            <option value="1">Blast tabular output + aligned sequences</option>
+            <option value="2">FASTA format. NOTE: Hit sequence only, without gaps !</option>
+            <option value="3">MAF format. NOTE: Header truncated to 30 characters!</option>
+            <option value="4">BED + aligned sequences</option>
+            <option value="5">GFF + aligned sequences</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output0" format="tabular" label="${tool.name} on ${on_string}">
+            <filter>o == '0'</filter>
+        </data>
+        <data name="output1" format="tabular" label="${tool.name} on ${on_string}">
+            <filter>o == '1'</filter>
+        </data>
+        <data name="output2" format="fasta" label="${tool.name} on ${on_string}">
+            <filter>o == '2'</filter>
+        </data>
+        <data name="output3" format="maf" label="${tool.name} on ${on_string}">
+            <filter>o == '3'</filter>
+        </data>
+        <data name="output4" format="bed" label="${tool.name} on ${on_string}">
+            <filter>o == '4'</filter>
+        </data>
+        <data name="output5" format="gff" label="${tool.name} on ${on_string}">
+            <filter>o == '5'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="dbase" value="NC_000913.fna"/>
+            <param name="query" value="C0299.fa"/>
+            <param name="o" value="2"/>
+            <output name="" ftype="fasta" file="gotohscan.result1"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**GotohScan** is a search tool that finds shorter sequences
+(usually genes) in large database sequences (chromosomes, genomes, ..)
+by computing all semi-global alignments.  Thus, the query sequence is
+never truncated or split into subsequences, but always mapped to the
+database over its complete length. The alignment is computed via the
+Gotoh-alignment algorithm using affine gap costs.
+]]></help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkn1084</citation>
+    </citations>
+</tool>