--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protxml_to_gff.xml	Thu Mar 26 20:11:34 2015 -0400
@@ -0,0 +1,102 @@
+<tool id="protxml_to_gff" name="Proteomics to GFF" version="1.1.0">
+	<description>Export Proteomics Data to GFF</description>
+
+	<requirements>
+		<container type="docker">iracooke/protk-1.4.1</container>		
+		<requirement type="package" version="1.4">protk</requirement>
+		<requirement type="package" version="2.2.29">blast+</requirement>
+   </requirements>
+
+	<command>
+		protxml_to_gff.rb $protxml_file 
+		
+		#if $database.source_select=="built_in":
+		-d $database.dbkey
+		#else 
+		-d $database.fasta_file
+		#end if
+
+		-c $gene_file
+
+		--gff-idregex='$gffidpattern'
+		
+		-o $output
+
+
+	</command>
+
+	<stdio>
+		<exit_code range="1:"   level="fatal"   description="Failure" />
+	</stdio>
+
+	<inputs>	
+		<conditional name="database">
+			<param name="source_select" type="select" label="Database source used for Proteomics Searches" help="Database should be an amino acid fasta file with entry id's that can be parsed to obtain contig or scaffold ids referenced in your gff file">
+				<option value="input_ref">Your Upload File</option>
+				<option value="built_in">Built-In</option>
+			</param>
+			<when value="built_in">
+				<param name="dbkey" type="select" format="text" >
+					<label>Database</label>
+					<options from_file="pepxml_databases.loc">
+						<column name="name" index="0" />
+						<column name="value" index="2" />
+					</options>
+				</param>
+			</when>
+			<when value="input_ref">
+				<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
+			</when>
+		</conditional>
+		
+		<param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/>
+
+		<param name="gene_file" type="data" format="gff3" multiple="false" label="Protein coordinates" help="A gff3 file with coordinates for all protein entries used for proteomics searches. Coordinates should correspond to entries in the genome fasta file"/>
+
+		<param name="gffidpattern" size="40" type="text" value="lcl\|([^ ]*)" label="gff id regex" help="Regex with capture group for parsing gff ids from protein ids">
+	    	<sanitizer>
+        	<valid initial="string.printable">
+         	<remove value="&apos;"/>
+        	</valid>
+        	<mapping initial="none">
+          	<add source="&apos;" target="__sq__"/>
+        	</mapping>
+      		</sanitizer>
+	    </param>
+
+	</inputs>
+
+	<outputs>
+		<data format="gff3" name="output" />
+	</outputs>
+
+
+	<tests>
+	  <test>
+	  	<param name="source_select" value="input_ref"/>
+	  	<param name="fasta_file" value="small_prot.fasta" format="fasta"/>
+
+	      <param name="protxml_file" value="small.prot.xml" format="protxml"/>
+	      <param name="gene_file" value="small_combined.gff" format="gff3"/>
+	      <output name="output" format="gff3">
+	          <assert_contents>
+	              <has_text text="polypeptide" />
+	          </assert_contents>
+	      </output>
+	  </test>
+	</tests>
+
+  <help>
+
+**What it does**
+
+Exports peptides and proteins to gff
+
+----
+
+**References**
+
+
+  </help>
+
+</tool>