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comparison FileInfo.xml @ 13:e8dce5e07fa5 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 19:45:10 +0000
parents 98f171dab07c
children 4af67edd5aef
comparison
equal deleted inserted replaced
12:32264aaa27b8 13:e8dce5e07fa5
52 <configfiles> 52 <configfiles>
53 <inputs name="args_json" data_style="paths"/> 53 <inputs name="args_json" data_style="paths"/>
54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
55 </configfiles> 55 </configfiles>
56 <inputs> 56 <inputs>
57 <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml data sets(s)"/> 57 <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,trafoxml data sets(s)"/>
58 <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/> 58 <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
59 <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/> 59 <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
60 <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/> 60 <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/>
61 <param name="d" argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/> 61 <param name="d" argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/>
62 <param name="c" argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/> 62 <param name="c" argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/>
63 <param name="v" argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/> 63 <param name="v" argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/>
64 <param name="i" argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/> 64 <param name="i" argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/>
65 <expand macro="adv_opts_macro"> 65 <expand macro="adv_opts_macro">
66 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 66 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
67 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 67 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
68 <expand macro="list_string_san"/> 68 <expand macro="list_string_san"/>
69 </param> 69 </param>
70 </expand> 70 </expand>
71 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 71 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
72 <option value="out_tsv_FLAG">out_tsv (Enables the test mode (needed for internal use only))</option> 72 <option value="out_tsv_FLAG">out_tsv (Second optional output file)</option>
73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
74 </param> 74 </param>
75 </inputs> 75 </inputs>
76 <outputs> 76 <outputs>
77 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/> 77 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
87 <expand macro="manutest_FileInfo"/> 87 <expand macro="manutest_FileInfo"/>
88 </tests> 88 </tests>
89 <help><![CDATA[Shows basic information about the file, such as data ranges and file type. 89 <help><![CDATA[Shows basic information about the file, such as data ranges and file type.
90 90
91 91
92 For more information, visit http://www.openms.de/documentation/TOPP_FileInfo.html]]></help> 92 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FileInfo.html]]></help>
93 <expand macro="references"/> 93 <expand macro="references"/>
94 </tool> 94 </tool>