Mercurial > repos > galaxyp > openms_mssimulator
comparison MSSimulator.xml @ 15:ad1ad0e62a92 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 18:51:30 +0000 |
| parents | 140b883daa61 |
| children |
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| 14:ec0cf8bcd350 | 15:ad1ad0e62a92 |
|---|---|
| 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> |