<ttd>
	<tool status="external">
		<category>Identification</category>
		// multiple of these are allowed
		<type>Percolator</type>
		#name# -- for internal use only
		// multiple of these allowed (same # as 'types') - for external only
		<external>
      <text>
        <onstartup>Running Percolator...</onstartup>
        <onfail>Something went wrong. Is the Percolator executable globally accessible?</onfail>
        <onfinish>Percolator finished successfully.</onfinish>
      </text>    
		  <e_category>Identification</e_category>
		  <cloptions>--only-psms --results-psms "%2" --decoy-results-psms "%3" "%1"</cloptions>
		  <path>percolator</path>
		  <workingdirectory>.</workingdirectory>
		  <mappings>
			<mapping id="1" cl="%%in" />
			<mapping id="2" cl="%TMP/%BASENAME[%%in].psms" />
			<mapping id="3" cl="%TMP/%BASENAME[%%in]_decoy.psms" />
			<file_post location="%TMP/%BASENAME[%%in].psms" target="out" />
			<file_post location="%TMP/%BASENAME[%%in]_decoy.psms" target="out_decoy" />
		  </mappings>
		  <ini_param>
			<ITEM name="in" value="" type="string" description="Input file: Percolator tab-delimited input (valid formats: 'csv')" tags="input file" />
			<ITEM name="out" value="" type="string" description="Output file: Percolator tab-delimited output, target hits (valid formats: 'psms')" tags="output file" />
			<ITEM name="out_decoy" value="" type="string" description="Output file: Percolator tab-delimited output, decoy hits (valid formats: 'psms')" tags="output file" />
		  </ini_param>
		</external>
	</tool>
</ttd>
