Mercurial > repos > galaxyp > openms_fileconverter

comparison FileConverter.xml @ 13:62e19948b50f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:48:09 +0000
parents f2388622d581
children 2a93a25f0599
comparison
equal deleted inserted replaced
12:9939af9b0ea3 13:62e19948b50f
75 <param name="write_scan_index" argument="-write_scan_index" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Append an index when writing mzML or mzXML files" help="Some external tools might rely on it"/> 75 <param name="write_scan_index" argument="-write_scan_index" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Append an index when writing mzML or mzXML files" help="Some external tools might rely on it"/>
76 <param name="lossy_compression" argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="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)" help=""/> 76 <param name="lossy_compression" argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="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)" help=""/>
77 <param name="lossy_mass_accuracy" argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/> 77 <param name="lossy_mass_accuracy" argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
78 <param name="process_lowmemory" argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/> 78 <param name="process_lowmemory" argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/>
79 <param name="no_peak_picking" argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/> 79 <param name="no_peak_picking" argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/>
80 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 80 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
81 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 81 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
82 <expand macro="list_string_san"/> 82 <expand macro="list_string_san"/>
83 </param> 83 </param>
84 </expand> 84 </expand>
85 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
87 </param> 87 </param>
88 </inputs> 88 </inputs>
89 <outputs> 89 <outputs>
90 <data name="out" label="${tool.name} on ${on_string}: out"> 90 <data name="out" label="${tool.name} on ${on_string}: out">
109 <expand macro="manutest_FileConverter"/> 109 <expand macro="manutest_FileConverter"/>
110 </tests> 110 </tests>
111 <help><![CDATA[Converts between different MS file formats. 111 <help><![CDATA[Converts between different MS file formats.
112 112
113 113
114 For more information, visit http://www.openms.de/documentation/TOPP_FileConverter.html]]></help> 114 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FileConverter.html]]></help>
115 <expand macro="references"/> 115 <expand macro="references"/>
116 </tool> 116 </tool>