--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spaln.xml	Fri Jan 11 18:15:21 2019 -0500
@@ -0,0 +1,84 @@
+<tool id="spaln" name="Spaln: align cDNA or Protein to genome" version="@TOOL_VERSION@+galaxy0">
+    <description>Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.3.2</token>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_3512</edam_topic>
+    </edam_topics>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">spaln</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+	    spaln -t\${GALAXY_SLOTS:-1} -O$format -o '$output1' '$genome' '$query'
+    ]]></command>
+    <inputs>
+        <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" />
+        <param type="data" name="query" format="fasta" label="Query sequence(s) (protein or cDNA)" />
+	<param argument="-O" type="select" name="format" label="Output format">
+	    <option value="0">GFF3 format genes</option>
+	    <option value="2">GFF3 format matches</option>
+	    <option value="3">BED format</option>
+	    <option value="4">Tabular format exon information</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular">
+	    <change_format>
+            <!-- these values correspond with the format options of the spaln command, not all of which are current supported -->
+            <when input="format" value="0" format="gff3" />
+            <when input="format" value="2" format="gff3" />
+            <when input="format" value="3" format="bed12" />
+            <when input="format" value="4" format="tabular" />
+	    </change_format>
+	    <!-- <actions> .. <conditional> .. <when> .. <action> current does not work in Galaxy,
+		 something that https://github.com/galaxyproject/galaxy/pull/7197 is addressing, so this is
+                 commented out till that is merged 
+	    <actions>
+	        <conditional name="format">
+		    <when value="4">
+                        <action type="metadata" name="column_names" default="rID,gID,%id,ExonL,MisMch,Unpair,ref_l,ref_r,tgt_l,tgt_r,eScore,IntrnL,iScore,Sig3/I,Sig5/T  # -  X P DiNuc" />
+		    </when>
+		</conditional>
+	    </actions>
+            -->
+	</data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="genome" ftype="fasta" value="genome.fasta" />
+            <param name="query" ftype="fasta" value="query.fasta" />
+            <param name="format" value="0"/>
+	        <output name="output1" value="output1_gff_genes.gff3" />
+        </test>
+        <test>
+            <param name="genome" ftype="fasta" value="genome.fasta" />
+            <param name="query" ftype="fasta" value="query.fasta" />
+            <param name="format" value="2"/>
+	        <output name="output1" value="output1_gff_matches.gff3" />
+        </test>
+        <test>
+            <param name="genome" ftype="fasta" value="genome.fasta" />
+            <param name="query" ftype="fasta" value="query.fasta" />
+            <param name="format" value="3"/>
+	        <output name="output1" value="output1.bed12" />
+        </test>
+        <test>
+            <param name="genome" ftype="fasta" value="genome.fasta" />
+            <param name="query" ftype="fasta" value="query.fasta" />
+            <param name="format" value="4"/>
+	        <output name="output1" value="output1.tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Spaln_ (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or
+        protein sequences onto a whole genomic sequence in a single job. 
+
+        This Galaxy wrapper currently only supports the default (i.e. *-O3*) algorithm for Spaln with default parameters.
+
+        .. _Spaln: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/
+    ]]></help>
+    <citations>
+        <citation type="doi">0.1093/nar/gkn105</citation>
+    </citations>
+</tool>