<ttd>
	<tool status="external">
		<category>Identification</category>
		// multiple of these are allowed
		<type>MascotPercolator</type>
		#name# -- for internal use only
		// multiple of these allowed (same # as 'types') - for external only
		<external>
      <text>
        <onstartup>Running Mascot Percolator...</onstartup>
        <onfail>Something went wrong. Is Java 8 available?</onfail>
        <onfinish>Mascot Percolator finished successfully.</onfinish>
      </text>    
		  <e_category>Identification</e_category>
		  <cloptions>-Xmx%6m -cp "%5" cli.MascotPercolator -i1 -newDat -overwrite -summary -u -target "%1" -decoy "%2" -out "%3" -decoypattern "%4"</cloptions>
		  <path>java</path>
		  <workingdirectory>.</workingdirectory>
		  <mappings>
			<mapping id="1" cl="%%in" />
			<mapping id="2" cl="%%in_decoy" />
			<mapping id="3" cl="%TMP/%BASENAME[%%in]" />
            <mapping id="4" cl="%%decoy_pattern" />
            <mapping id="5" cl="%%jar" />
            <mapping id="6" cl="%%java_memory" />
			<file_post location="%TMP/%BASENAME[%%in].psms" target="out" />
			<file_post location="%TMP/%BASENAME[%%in]_decoy.psms" target="out_decoy" />
			<file_post location="%TMP/%BASENAME[%%in].summary.txt" target="out_summary" />
			<file_post location="%TMP/%BASENAME[%%in].summary_decoy.txt" target="out_summary_decoy" />
			<file_post location="%TMP/%BASENAME[%%in].datp" target="out_dat" />
          </mappings>
		  <ini_param>
			<ITEM name="in" value="" type="string" description="Input file: Mascot search results from MascotAdapterOnline; either from a combined target/decoy search (then set 'decoy_pattern') or from a target-only search (then set 'in_decoy') (valid formats: 'idXML')" tags="input file" />
			<ITEM name="in_decoy" value="TARGET" type="string" description="Input file: Mascot decoy-only search results from MascotAdapterOnline, or 'TARGET' for a concatenated target/decoy search passed via 'in_target' (valid formats: 'idXML')" tags="input file" />
			<ITEM name="jar" value="MascotPercolator.jar" type="string" description="Mascot Percolator .jar file (valid formats: 'jar')" 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" />
			<ITEM name="out_summary" value="" type="string" description="Output file: Mascot Percolator tab-delimited output, target summary (valid formats: 'txt')" tags="output file" />
			<ITEM name="out_summary_decoy" value="" type="string" description="Output file: Mascot Percolator tab-delimited output, decoy summary (valid formats: 'txt')" tags="output file" />
			<ITEM name="out_dat" value="" type="string" description="Output file: Mascot DAT file with Percolator scores (valid formats: 'datp')" tags="output file" />
            <ITEM name="decoy_pattern" value="DECOY_" type="string" description="Pattern identifying decoy matches. Only used if 'in_decoy' is 'TARGET', but must not be empty!" />
            <ITEM name="java_memory" value="1024" type="string" description="Maximum Java heap size (in MB)" />            
		  </ini_param>
		</external>
	</tool>
</ttd>
