Mercurial > repos > galaxyp > openms_targetedfileconverter

comparison TargetedFileConverter.xml @ 9:6562463bf496 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:21:48 +0000
parents 51b9c2d5b4c3
children 9c70a651a53e
comparison
equal deleted inserted replaced
8:aa62f8f48dd4 9:6562463bf496
40 <inputs name="args_json" data_style="paths"/> 40 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 42 </configfiles>
43 <inputs> 43 <inputs>
44 <param name="in" argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/> 44 <param name="in" argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file select mrm,pqp,tabular,traml data sets(s)"/>
45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense"> 45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: not all conversion paths work or make sense">
46 <option value="TraML">traml</option> 46 <option value="TraML">traml</option>
47 <option value="pqp">pqp</option> 47 <option value="pqp">pqp</option>
48 <option value="tsv">tabular (tsv)</option> 48 <option value="tsv">tabular (tsv)</option>
49 <expand macro="list_string_san"/> 49 <expand macro="list_string_san"/>
50 </param> 50 </param>
58 <param name="override_group_label_check" argument="-algorithm:override_group_label_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="Only turn this off if you know what you are doing"/> 58 <param name="override_group_label_check" argument="-algorithm:override_group_label_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="Only turn this off if you know what you are doing"/>
59 <param name="force_invalid_mods" argument="-algorithm:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/> 59 <param name="force_invalid_mods" argument="-algorithm:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/>
60 </section> 60 </section>
61 <expand macro="adv_opts_macro"> 61 <expand macro="adv_opts_macro">
62 <param name="legacy_traml_id" argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" help=""/> 62 <param name="legacy_traml_id" argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" help=""/>
63 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 63 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
64 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 64 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
65 <expand macro="list_string_san"/> 65 <expand macro="list_string_san"/>
66 </param> 66 </param>
67 </expand> 67 </expand>
68 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 68 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
69 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 69 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
70 </param> 70 </param>
71 </inputs> 71 </inputs>
72 <outputs> 72 <outputs>
73 <data name="out" label="${tool.name} on ${on_string}: out"> 73 <data name="out" label="${tool.name} on ${on_string}: out">
86 <expand macro="manutest_TargetedFileConverter"/> 86 <expand macro="manutest_TargetedFileConverter"/>
87 </tests> 87 </tests>
88 <help><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis. 88 <help><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis.
89 89
90 90
91 For more information, visit http://www.openms.de/documentation/UTILS_TargetedFileConverter.html]]></help> 91 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_TargetedFileConverter.html]]></help>
92 <expand macro="references"/> 92 <expand macro="references"/>
93 </tool> 93 </tool>