<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>