Mercurial > repos > galaxyp > openms_idfileconverter

comparison IDFileConverter.xml @ 13:250d6a43f66b 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 19:44:49 +0000
parents 43a1db77b7a6
children 7d0eb300f360
comparison
equal deleted inserted replaced
12:6772d71b9150 13:250d6a43f66b
75 <expand macro="list_string_san"/> 75 <expand macro="list_string_san"/>
76 </param> 76 </param>
77 <param name="no_spectra_data_override" argument="-no_spectra_data_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="Use only if you are sure it is absolutely the same mz_file as used for identification"/> 77 <param name="no_spectra_data_override" argument="-no_spectra_data_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="Use only if you are sure it is absolutely the same mz_file as used for identification"/>
78 <param name="no_spectra_references_override" argument="-no_spectra_references_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Setting this flag will avoid overriding 'spectrum_reference' in PeptideIdentifications if mz_file is given and a 'spectrum_reference' is already present" help=""/> 78 <param name="no_spectra_references_override" argument="-no_spectra_references_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Setting this flag will avoid overriding 'spectrum_reference' in PeptideIdentifications if mz_file is given and a 'spectrum_reference' is already present" help=""/>
79 <param name="add_ionmatch_annotation" argument="-add_ionmatch_annotation" type="float" optional="true" value="0.0" label="[+mz_file only] Will annotate the contained identifications with their matches in the given mz_file" help="Will take quite some while. Match tolerance is .4"/> 79 <param name="add_ionmatch_annotation" argument="-add_ionmatch_annotation" type="float" optional="true" value="0.0" label="[+mz_file only] Will annotate the contained identifications with their matches in the given mz_file" help="Will take quite some while. Match tolerance is .4"/>
80 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 80 <param name="concatenate_peptides" argument="-concatenate_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[FASTA output only] Will concatenate the top peptide hits to one peptide sequence, rather than write a new peptide for each hit" help=""/>
81 <param name="number_of_hits" argument="-number_of_hits" type="integer" optional="true" value="1" label="[FASTA output only] Controls how many peptide hits will be exported" help="A value of 0 or less exports all hits"/>
82 <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=""> 83 <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"/> 84 <expand macro="list_string_san"/>
83 </param> 85 </param>
84 </expand> 86 </expand>
85 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 87 <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> 88 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
87 </param> 89 </param>
88 </inputs> 90 </inputs>
89 <outputs> 91 <outputs>
90 <data name="out" label="${tool.name} on ${on_string}: out"> 92 <data name="out" label="${tool.name} on ${on_string}: out">
105 <expand macro="manutest_IDFileConverter"/> 107 <expand macro="manutest_IDFileConverter"/>
106 </tests> 108 </tests>
107 <help><![CDATA[Converts identification engine file formats. 109 <help><![CDATA[Converts identification engine file formats.
108 110
109 111
110 For more information, visit http://www.openms.de/documentation/TOPP_IDFileConverter.html]]></help> 112 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDFileConverter.html]]></help>
111 <expand macro="references"/> 113 <expand macro="references"/>
112 </tool> 114 </tool>