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OpenMS
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Allows generically the wrapping of external tools.
pot. predecessor tools | → GenericWrapper → | pot. successor tools |
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any file the external tool can read | any tool reading the output format | |
IDFileConverter (to produce pepXML) | → GenericWrapper (type 'ProteinProphet') → | IDFileConverter (protXML to idXML) |
RAW file | → GenericWrapper (type 'RAWFileConvert') → | any tool accepting mzML |
This tool is a wrapper to call external (non-OpenMS) executables/scripts. Each supported tool is represented by a certain type
. Each type exposes certain parameters which you can set (usually at least a in
and out
).
To obtain support for more external programs, visit the OpenMS website or (if you cannot find your tool there) ask on the OpenMS mailing list.
The following section is for experts only, who want to add their own external tool:
Each external tool is configured via a wrapper XML file in 'OpenMS/share/OpenMS/TOOLS/EXTERNAL'. All files have the ending .ttd (TOPP tool description). You can add one or more wrappers (i.e. types) per file, but we recommend one. The filename does not really matter, but it should be descriptive.
The ttd file has the following structure:
type | The name of the type which is added to list of valid GenericWrapper types. It should be unique, otherwise you get a fatal error. |
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category | Category for TOPPAS. |
cloptions | Command line options (arguments) appended to the executable. This string might contain placeholders of the form "%<i>" where each placeholder will be substituted with a value that is determined in the mappings section (see below). Example: <cloptions>-o "%1" --mzML "%2"</cloptions>
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path | Path (can be relative) to the executable that is executed. |
mappings | Used to replace placeholders with input parameters. The mapping id corresponds to the placeholder in
Example: <mapping id="2" cl="-output_file %BASENAME[%%in].mgf -temp_dir %TMP -depth 3" />
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ini_param | Contains part of a normal INI file with describes the parameters. Valid tags are those that are in the ParamXML scheme below 'NODE', e.g. 'ITEM'. Example: <ITEM name="out" value="" type="string" description="output XML file containg regression line and confidence interval" tags="output file" />
<ITEM name="mz_tolerance" value="1" type="float" description="Tolerance in m/z dimension" />
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The command line parameters of this tool are:
INI file documentation of this tool: