Mercurial > repos > galaxyp > openms_mssimulator

comparison MSSimulator.xml @ 11:04228172e123 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 20:12:16 +0000
parents 98bb49e7b5ba
children 9e6a371d539b
comparison
equal deleted inserted replaced
10:6edc2f116865 11:04228172e123
113 <param name="in" argument="-in" type="data" format="fasta" multiple="true" optional="false" label="Input protein sequences" help=" select fasta data sets(s)"/> 113 <param name="in" argument="-in" type="data" format="fasta" multiple="true" optional="false" label="Input protein sequences" help=" select fasta data sets(s)"/>
114 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 114 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
115 <section name="MSSim" title="" help="" expanded="false"> 115 <section name="MSSim" title="" help="" expanded="false">
116 <section name="Digestion" title="" help="" expanded="false"> 116 <section name="Digestion" title="" help="" expanded="false">
117 <param name="enzyme" argument="-algorithm:MSSim:Digestion:enzyme" type="select" optional="false" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help=""> 117 <param name="enzyme" argument="-algorithm:MSSim:Digestion:enzyme" type="select" optional="false" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="">
118 <option value="PepsinA">PepsinA</option> 118 <option value="Trypsin/P">Trypsin/P</option>
119 <option value="TrypChymo">TrypChymo</option> 119 <option value="V8-DE">V8-DE</option>
120 <option value="Arg-C">Arg-C</option> 120 <option value="V8-E">V8-E</option>
121 <option value="Arg-C/P">Arg-C/P</option> 121 <option value="leukocyte elastase">leukocyte elastase</option>
122 <option value="Asp-N">Asp-N</option>
123 <option value="Asp-N/B">Asp-N/B</option> 122 <option value="Asp-N/B">Asp-N/B</option>
124 <option value="Asp-N_ambic">Asp-N_ambic</option> 123 <option value="Asp-N_ambic">Asp-N_ambic</option>
125 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
126 <option value="no cleavage">no cleavage</option>
127 <option value="unspecific cleavage">unspecific cleavage</option>
128 <option value="proline endopeptidase">proline endopeptidase</option>
129 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
130 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
131 <option value="2-iodobenzoate">2-iodobenzoate</option>
132 <option value="Chymotrypsin">Chymotrypsin</option> 124 <option value="Chymotrypsin">Chymotrypsin</option>
133 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 125 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
134 <option value="CNBr">CNBr</option> 126 <option value="CNBr">CNBr</option>
135 <option value="Formic_acid">Formic_acid</option> 127 <option value="Formic_acid">Formic_acid</option>
136 <option value="Lys-C">Lys-C</option> 128 <option value="Lys-C">Lys-C</option>
137 <option value="Lys-N">Lys-N</option> 129 <option value="proline endopeptidase">proline endopeptidase</option>
138 <option value="Lys-C/P">Lys-C/P</option> 130 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
131 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
132 <option value="2-iodobenzoate">2-iodobenzoate</option>
139 <option value="iodosobenzoate">iodosobenzoate</option> 133 <option value="iodosobenzoate">iodosobenzoate</option>
140 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 134 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
141 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 135 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
142 <option value="Glu-C+P">Glu-C+P</option> 136 <option value="Glu-C+P">Glu-C+P</option>
143 <option value="PepsinA + P">PepsinA + P</option> 137 <option value="PepsinA + P">PepsinA + P</option>
144 <option value="cyanogen-bromide">cyanogen-bromide</option> 138 <option value="cyanogen-bromide">cyanogen-bromide</option>
145 <option value="Clostripain/P">Clostripain/P</option> 139 <option value="Clostripain/P">Clostripain/P</option>
146 <option value="Trypsin/P">Trypsin/P</option> 140 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
147 <option value="V8-DE">V8-DE</option> 141 <option value="Arg-C">Arg-C</option>
148 <option value="V8-E">V8-E</option> 142 <option value="Arg-C/P">Arg-C/P</option>
149 <option value="leukocyte elastase">leukocyte elastase</option> 143 <option value="Asp-N">Asp-N</option>
144 <option value="no cleavage">no cleavage</option>
145 <option value="unspecific cleavage">unspecific cleavage</option>
146 <option value="Lys-N">Lys-N</option>
147 <option value="Lys-C/P">Lys-C/P</option>
148 <option value="PepsinA">PepsinA</option>
149 <option value="TrypChymo">TrypChymo</option>
150 <option value="Trypsin" selected="true">Trypsin</option> 150 <option value="Trypsin" selected="true">Trypsin</option>
151 <expand macro="list_string_san"/> 151 <expand macro="list_string_san"/>
152 </param> 152 </param>
153 <param name="model" argument="-algorithm:MSSim:Digestion:model" display="radio" type="select" optional="false" label="The cleavage model to use for digestion" help="'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)"> 153 <param name="model" argument="-algorithm:MSSim:Digestion:model" display="radio" type="select" optional="false" label="The cleavage model to use for digestion" help="'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
154 <option value="trained">trained</option> 154 <option value="trained">trained</option>
508 <expand macro="list_string_san"/> 508 <expand macro="list_string_san"/>
509 </param> 509 </param>
510 </section> 510 </section>
511 </section> 511 </section>
512 <expand macro="adv_opts_macro"> 512 <expand macro="adv_opts_macro">
513 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 513 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
514 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 514 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
515 <expand macro="list_string_san"/> 515 <expand macro="list_string_san"/>
516 </param> 516 </param>
517 </expand> 517 </expand>
518 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> 518 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
519 <option value="out_FLAG">out (Controls the 'technical' randomness of the generated data)</option> 519 <option value="out_FLAG">out (output: simulated MS raw (profile) data)</option>
520 <option value="out_pm_FLAG">out_pm (Controls the 'technical' randomness of the generated data)</option> 520 <option value="out_pm_FLAG">out_pm (output: ground-truth picked (centroided) MS data)</option>
521 <option value="out_fm_FLAG">out_fm (Controls the 'technical' randomness of the generated data)</option> 521 <option value="out_fm_FLAG">out_fm (output: ground-truth features)</option>
522 <option value="out_cm_FLAG">out_cm (Controls the 'technical' randomness of the generated data)</option> 522 <option value="out_cm_FLAG">out_cm (output: ground-truth features, grouping ESI charge variants of each parent peptide)</option>
523 <option value="out_lcm_FLAG">out_lcm (Controls the 'technical' randomness of the generated data)</option> 523 <option value="out_lcm_FLAG">out_lcm (output: ground-truth features, grouping labeled variants)</option>
524 <option value="out_cntm_FLAG">out_cntm (Controls the 'technical' randomness of the generated data)</option> 524 <option value="out_cntm_FLAG">out_cntm (output: ground-truth features caused by contaminants)</option>
525 <option value="out_id_FLAG">out_id (Controls the 'technical' randomness of the generated data)</option> 525 <option value="out_id_FLAG">out_id (output: ground-truth MS2 peptide identifications)</option>
526 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 526 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
527 </param> 527 </param>
528 </inputs> 528 </inputs>
529 <outputs> 529 <outputs>
530 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"> 530 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml">
560 <expand macro="manutest_MSSimulator"/> 560 <expand macro="manutest_MSSimulator"/>
561 </tests> 561 </tests>
562 <help><![CDATA[A highly configurable simulator for mass spectrometry experiments. 562 <help><![CDATA[A highly configurable simulator for mass spectrometry experiments.
563 563
564 564
565 For more information, visit http://www.openms.de/documentation/UTILS_MSSimulator.html]]></help> 565 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSSimulator.html]]></help>
566 <expand macro="references"/> 566 <expand macro="references"/>
567 </tool> 567 </tool>