<ttd>
	<tool status="external">
		<category>Identification</category>
		// multiple of these are allowed
		<type>MSGFtoPercolator</type>
		#name# -- for internal use only
		// multiple of these allowed (same # as 'types') - for external only
		<external>
      <text>
        <onstartup>Running "msgf2pin" converter...</onstartup>
        <onfail>Something went wrong. Is the msgf2pin executable globally accessible?</onfail>
        <onfinish>msgf2pin finished successfully.</onfinish>
      </text>    
		  <e_category>Identification</e_category>
		  <cloptions>--pattern "%4" --outputTab "%3" "%1" "%2"</cloptions>
		  <path>msgf2pin</path>
		  <workingdirectory>.</workingdirectory>
		  <mappings>
			<mapping id="1" cl="%%in" />
			<mapping id="2" cl="%%in_decoy" />
			<mapping id="3" cl="%%out" />
            <mapping id="4" cl="%%decoy_pattern" />
		  </mappings>
		  <ini_param>
			<ITEM name="in" value="" type="string" description="Input file: MS-GF+ search results; either from a combined target/decoy search (then set 'decoy_pattern') or from a target-only search (then set 'in_decoy') (valid formats: 'mzid')" tags="input file" />
			<ITEM name="in_decoy" value="" type="string" description="Input file: MS-GF+ search results; from a decoy-only search (valid formats: 'mzid')" tags="input file" />
			<ITEM name="out" value="" type="string" description="Output file: Percolator tab-delimited input (valid formats: 'csv')" tags="output file" />
            <ITEM name="decoy_pattern" value="DECOY_" type="string" description="Pattern identifying decoy matches. Ignored if 'in_decoy' is set, but must not be empty!" />
            <ITEM name="enzyme" value="trypsin" type="string" description="Enzyme used for digestion" restrictions="no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin" />
		  </ini_param>
		</external>
	</tool>
</ttd>
