<ttd>
	<tool status="external">
		<category>does not really matter</category>
		<!-- this is the name of the '-type' which is added to GenericWrapper - so chose carefully -->
		<type>RAWFileConvert</type>
		<!-- description of the wrapper -->
		<external>
      <text>
        <onstartup>This is printed on startup ... Wrapper was tested with "external_tool" vX.Y.Z, report issues to the OpenMS team at www.OpenMS.de</onstartup>
        <onfail>This is printed in case of error - you can list possible causes for failure here...</onfail>
        <onfinish>This is printed when finished successfully.</onfinish>
      </text>    
		  <!-- currently disregarded by TOPPAS, but might become useful -->
		  <e_category>FileConversion</e_category>
		  <!-- command line options of your external tool (use placeholders ,e.g. %1 to insert dynamic content)
           You should quote placeholders which hold single files, but avoid quotes for lists (ITEMLIST in ini_param section), since they are quoted by GenericWrapper
           automatically -->
		  <cloptions>-o "%1" --mzML "%2"</cloptions>
		  <!-- the actual executable (usually it should be in your PATH, to avoid having to specify a full path to it) -->
		  <path>msconvert</path>
      <!-- sets the working directory to this path before calling the external tool. Some tools write to the current working directory
           and thus starting the tool from somewhere else might actually lead to trouble
           use only real paths here (no placeholders like %TMP) -->
      <workingdirectory>.</workingdirectory>
		  <!-- these mappings connect input parameters (from the 'ini_param' section below) and the command line options of your tool
		       any INI parameter can be referenced using %%'param_name', e.g. %%in
		       additionally you can use %TMP and %BASENAME[X] to get the current temp directory to store data, or the basename of X -->
		  <mappings>
			<mapping id="1" cl="%TMP" />
			<mapping id="2" cl="%%in" />

			<!-- input mapping/copying: this is a little hard to explain and usually you will not need it (delete all file-tags of the parameter!)
			     what it does: when the wrapped tool works with in-place files (i.e. overwrites its input), you must copy it before invoking the tool,
			                   e.g. TPP's RefreshParser will overwrite its input pepXML file
			                   The targeted parameter gets replaced with a temporary filename after the copy is done, so that subsequent
			                   operations target the temp file -->
      <file_pre location="%TMP/%RND_%%in" target="in" />
      
			<!-- output mapping/moving: this is a little hard to explain and usually you will not need it (delete all file-tags of the parameter!)
			     what it does: when you cannot specify an explicit output file to the external tool and it rather determines that by itself,
			                   e.g. msconvert will create an output file (call it F) which has the same name as the input file with a replaced suffix
			                   then you might need to move F to the name specified in 'out' (or any other parameter)
			                   Thus you specify the name of F and the name of the target parameter (in terms of INI parameter values) -->
			<file_post location="%TMP/%BASENAME[%%in].mzML" target="out" />
		  </mappings>
		  <ini_param>
			<ITEM name="in" value="" type="string" description="input file in RAW format(valid formats: &apos;RAW&apos;)" tags="input file" />
			<ITEM name="out" value="" type="string" description="output file in mzML format(valid formats: &apos;mzML&apos;)" tags="output file" />
		  </ini_param>
		</external>
	</tool>
</ttd>
