Mercurial > repos > galaxyp > openms_spectrastsearchadapter

comparison SpectraSTSearchAdapter.xml @ 10:27ddea86fe90 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 19:50:42 +0000
parents 28e96ae21a44
children 4d189842ebfc
comparison
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9:7e2e9379aec7 10:27ddea86fe90
71 <configfiles> 71 <configfiles>
72 <inputs name="args_json" data_style="paths"/> 72 <inputs name="args_json" data_style="paths"/>
73 <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 73 <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
74 </configfiles> 74 </configfiles>
75 <inputs> 75 <inputs>
76 <param name="spectra_files" argument="-spectra_files" type="data" format="dta,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,msp,mzdata,mzml,mzxml data sets(s)"/> 76 <param name="spectra_files" argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
77 <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)"> 77 <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)">
78 <option value="txt">txt</option> 78 <option value="txt">txt</option>
79 <option value="tsv">tabular (tsv)</option> 79 <option value="tsv">tabular (tsv)</option>
80 <option value="pep.xml">pepxml (pep.xml)</option> 80 <option value="pep.xml">pepxml (pep.xml)</option>
81 <option value="xml">xml</option>
82 <option value="pepXML">pepxml</option> 81 <option value="pepXML">pepxml</option>
83 <option value="html">html</option> 82 <option value="html">html</option>
84 </param> 83 </param>
85 <param name="library_file" argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/> 84 <param name="library_file" argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
86 <param name="sequence_database_file" argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/> 85 <param name="sequence_database_file" argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/>
93 <param name="precursor_mz_tolerance" argument="-precursor_mz_tolerance" type="float" optional="true" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/> 92 <param name="precursor_mz_tolerance" argument="-precursor_mz_tolerance" type="float" optional="true" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/>
94 <expand macro="adv_opts_macro"> 93 <expand macro="adv_opts_macro">
95 <param name="use_isotopically_averaged_mass" argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/> 94 <param name="use_isotopically_averaged_mass" argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/>
96 <param name="use_all_charge_states" argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/> 95 <param name="use_all_charge_states" argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/>
97 <param name="user_mod_file" argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/> 96 <param name="user_mod_file" argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/>
98 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 97 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
99 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 98 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
100 <expand macro="list_string_san"/> 99 <expand macro="list_string_san"/>
101 </param> 100 </param>
102 </expand> 101 </expand>
103 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 102 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
104 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 103 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
105 </param> 104 </param>
106 </inputs> 105 </inputs>
107 <outputs> 106 <outputs>
108 <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files"> 107 <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
117 <expand macro="manutest_SpectraSTSearchAdapter"/> 116 <expand macro="manutest_SpectraSTSearchAdapter"/>
118 </tests> 117 </tests>
119 <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable 118 <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable
120 119
121 120
122 For more information, visit http://www.openms.de/documentation/UTILS_SpectraSTSearchAdapter.html]]></help> 121 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
123 <expand macro="references"/> 122 <expand macro="references"/>
124 </tool> 123 </tool>