Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

comparison ctd/FileConverter.ctd @ 18:6daaa75ccb99 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
author galaxyp
date Sun, 13 Dec 2020 15:03:50 +0000
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17:6f6c1cb968a0 18:6daaa75ccb99
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool ctdVersion="1.7" version="2.6.0-pre-exported-20201001" name="FileConverter" docurl="http://www.openms.de/documentation/TOPP_FileConverter.html" category="File Handling" >
3 <description><![CDATA[Converts between different MS file formats.]]></description>
4 <manual><![CDATA[Converts between different MS file formats.]]></manual>
5 <citations>
6 <citation doi="10.1038/nmeth.3959" url="" />
7 </citations>
8 <PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
9 <NODE name="FileConverter" description="Converts between different MS file formats.">
10 <ITEM name="version" value="2.6.0-pre-exported-20201001" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
11 <NODE name="1" description="Instance &apos;1&apos; section for &apos;FileConverter&apos;">
12 <ITEM name="in" value="" type="input-file" description="Input file to convert." required="true" advanced="false" supported_formats="*.mzML,*.mzXML,*.mgf,*.raw,*.cachedMzML,*.mzData,*.dta,*.dta2d,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta" />
13 <ITEM name="in_type" value="" type="string" description="Input file type -- default: determined from file extension or content#br#" required="false" advanced="true" restrictions="mzML,mzXML,mgf,raw,cachedMzML,mzData,dta,dta2d,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta" />
14 <ITEM name="UID_postprocessing" value="ensure" type="string" description="unique ID post-processing for output data.#br#&apos;none&apos; keeps current IDs even if invalid.#br#&apos;ensure&apos; keeps current IDs but reassigns invalid ones.#br#&apos;reassign&apos; assigns new unique IDs." required="false" advanced="true" restrictions="none,ensure,reassign" />
15 <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.mzXML,*.cachedMzML,*.mgf,*.featureXML,*.consensusXML,*.edta,*.mzData,*.dta2d,*.csv" />
16 <ITEM name="out_type" value="" type="string" description="Output file type -- default: determined from file extension or content#br#Note: that not all conversion paths work or make sense." required="false" advanced="true" restrictions="mzML,mzXML,cachedMzML,mgf,featureXML,consensusXML,edta,mzData,dta2d,csv" />
17 <ITEM name="TIC_DTA2D" value="false" type="bool" description="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions." required="false" advanced="true" />
18 <ITEM name="MGF_compact" value="false" type="bool" description="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" required="false" advanced="true" />
19 <ITEM name="force_MaxQuant_compatibility" value="false" type="bool" description="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to &apos;Thermo Scientific&apos;." required="false" advanced="true" />
20 <ITEM name="convert_to_chromatograms" value="false" type="bool" description="[mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data." required="false" advanced="true" />
21 <ITEM name="force_TPP_compatibility" value="false" type="bool" description="[mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)." required="false" advanced="true" />
22 <ITEM name="change_im_format" value="none" type="string" description="[mzML output only] How to store ion mobility scans (none: no change in format, multiple: store each frame as multiple scans, one per drift time value, single: store whole frame as single scan with IM values in a FloatDataArray" required="false" advanced="true" restrictions="none,multiple,single" />
23 <ITEM name="write_scan_index" value="true" type="string" description="Append an index when writing mzML or mzXML files. Some external tools might rely on it." required="false" advanced="true" restrictions="true,false" />
24 <ITEM name="lossy_compression" value="false" type="bool" description="Use numpress compression to achieve optimally small file size using linear compression for m/z domain and slof for intensity and float data arrays (attention: may cause small loss of precision; only for mzML data)." required="false" advanced="true" />
25 <ITEM name="lossy_mass_accuracy" value="-1.0" type="double" description="Desired (absolute) m/z accuracy for lossy compression (e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)." required="false" advanced="true" />
26 <ITEM name="process_lowmemory" value="false" type="bool" description="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).#br#Note: this flag will prevent conversion from spectra to chromatograms." required="false" advanced="true" />
27 <ITEM name="NET_executable" value="" type="input-file" description="The .NET framework executable. Only required on linux and mac." required="false" advanced="true" />
28 <ITEM name="ThermoRaw_executable" value="ThermoRawFileParser.exe" type="input-file" description="The ThermoRawFileParser executable." required="false" advanced="true" supported_formats="*.exe" />
29 <ITEM name="no_peak_picking" value="false" type="bool" description="Disables vendor peak picking for raw files." required="false" advanced="true" />
30 <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
31 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
32 <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
33 <ITEM name="no_progress" value="false" type="bool" description="Disables progress logging to command line" required="false" advanced="true" />
34 <ITEM name="force" value="false" type="bool" description="Overrides tool-specific checks" required="false" advanced="true" />
35 <ITEM name="test" value="false" type="bool" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" />
36 </NODE>
37 </NODE>
38 </PARAMETERS>
39 </tool>