/usr/share/openms-common/OpenMS/TOOLS/EXTERNAL/TEMPLATE.ttd_ is in openms-common 1.11.1-3.
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<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)
<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" />
// output mapping/copying: this is a little hard to explain and usually you will not need it (then you have to delete all file-tags!)
// what it does: when the wrapped tool works with in-place files (i.e. overwrites its input), you must copy it before
// ,e.g. TPP's RefreshParser will overwrite its input pepXML file
// The targeted parameter gets replaced with the 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 (then you have to delete all file-tags!)
// 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_E) which has the same name as the input file with a replaced suffix
// then you might need to move F_E to the name you want (and/or where TOPPAS can find it)
// Thus you specify the name of F_E and the target name (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: 'RAW')" tags="input file" />
<ITEM name="out" value="" type="string" description="output file in mzML format(valid formats: 'mzML')" tags="output file" />
</ini_param>
</external>
</tool>
</ttd>
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