Mercurial > repos > galaxyp > openms_msfraggeradapter
comparison MSFraggerAdapter.xml @ 2:6bcc338b9dc6 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 20:09:43 +0000 |
| parents | 5a9c3e827da5 |
| children | e133b5c8878f |
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| 1:5a9c3e827da5 | 2:6bcc338b9dc6 |
|---|---|
| 87 <expand macro="list_string_san"/> | 87 <expand macro="list_string_san"/> |
| 88 </param> | 88 </param> |
| 89 </section> | 89 </section> |
| 90 <section name="digest" title="In-Silico Digestion Parameters" help="" expanded="false"> | 90 <section name="digest" title="In-Silico Digestion Parameters" help="" expanded="false"> |
| 91 <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" optional="false" label="Name of the enzyme to be written to the pepXML file" help=""> | 91 <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" optional="false" label="Name of the enzyme to be written to the pepXML file" help=""> |
| 92 <option value="staphylococcal protease/D">staphylococcal protease/D</option> | |
| 93 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> | |
| 94 <option value="Glu-C+P">Glu-C+P</option> | |
| 92 <option value="PepsinA + P">PepsinA + P</option> | 95 <option value="PepsinA + P">PepsinA + P</option> |
| 93 <option value="cyanogen-bromide">cyanogen-bromide</option> | 96 <option value="cyanogen-bromide">cyanogen-bromide</option> |
| 94 <option value="Clostripain/P">Clostripain/P</option> | 97 <option value="Clostripain/P">Clostripain/P</option> |
| 95 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> | 98 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> |
| 96 <option value="no cleavage">no cleavage</option> | 99 <option value="no cleavage">no cleavage</option> |
| 97 <option value="unspecific cleavage">unspecific cleavage</option> | 100 <option value="unspecific cleavage">unspecific cleavage</option> |
| 101 <option value="Arg-C">Arg-C</option> | |
| 102 <option value="Arg-C/P">Arg-C/P</option> | |
| 103 <option value="Lys-C">Lys-C</option> | |
| 104 <option value="Lys-N">Lys-N</option> | |
| 105 <option value="Lys-C/P">Lys-C/P</option> | |
| 106 <option value="PepsinA">PepsinA</option> | |
| 107 <option value="TrypChymo">TrypChymo</option> | |
| 108 <option value="Trypsin/P">Trypsin/P</option> | |
| 109 <option value="V8-DE">V8-DE</option> | |
| 110 <option value="V8-E">V8-E</option> | |
| 98 <option value="leukocyte elastase">leukocyte elastase</option> | 111 <option value="leukocyte elastase">leukocyte elastase</option> |
| 99 <option value="proline endopeptidase">proline endopeptidase</option> | 112 <option value="proline endopeptidase">proline endopeptidase</option> |
| 100 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> | 113 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> |
| 101 <option value="Alpha-lytic protease">Alpha-lytic protease</option> | 114 <option value="Alpha-lytic protease">Alpha-lytic protease</option> |
| 102 <option value="2-iodobenzoate">2-iodobenzoate</option> | 115 <option value="2-iodobenzoate">2-iodobenzoate</option> |
| 103 <option value="iodosobenzoate">iodosobenzoate</option> | 116 <option value="iodosobenzoate">iodosobenzoate</option> |
| 104 <option value="staphylococcal protease/D">staphylococcal protease/D</option> | |
| 105 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> | |
| 106 <option value="Glu-C+P">Glu-C+P</option> | |
| 107 <option value="Lys-C/P">Lys-C/P</option> | |
| 108 <option value="PepsinA">PepsinA</option> | |
| 109 <option value="Arg-C">Arg-C</option> | |
| 110 <option value="Arg-C/P">Arg-C/P</option> | |
| 111 <option value="Asp-N">Asp-N</option> | 117 <option value="Asp-N">Asp-N</option> |
| 112 <option value="Asp-N/B">Asp-N/B</option> | 118 <option value="Asp-N/B">Asp-N/B</option> |
| 113 <option value="Asp-N_ambic">Asp-N_ambic</option> | 119 <option value="Asp-N_ambic">Asp-N_ambic</option> |
| 114 <option value="Chymotrypsin">Chymotrypsin</option> | 120 <option value="Chymotrypsin">Chymotrypsin</option> |
| 115 <option value="Chymotrypsin/P">Chymotrypsin/P</option> | 121 <option value="Chymotrypsin/P">Chymotrypsin/P</option> |
| 116 <option value="CNBr">CNBr</option> | 122 <option value="CNBr">CNBr</option> |
| 117 <option value="Formic_acid">Formic_acid</option> | 123 <option value="Formic_acid">Formic_acid</option> |
| 118 <option value="Lys-C">Lys-C</option> | |
| 119 <option value="Lys-N">Lys-N</option> | |
| 120 <option value="TrypChymo">TrypChymo</option> | |
| 121 <option value="Trypsin/P">Trypsin/P</option> | |
| 122 <option value="V8-DE">V8-DE</option> | |
| 123 <option value="V8-E">V8-E</option> | |
| 124 <option value="Trypsin" selected="true">Trypsin</option> | 124 <option value="Trypsin" selected="true">Trypsin</option> |
| 125 <expand macro="list_string_san"/> | 125 <expand macro="list_string_san"/> |
| 126 </param> | 126 </param> |
| 127 <param name="search_enzyme_cutafter" argument="-digest:search_enzyme_cutafter" type="text" optional="true" value="KR" label="Residues after which the enzyme cuts (specified as a string of amino acids)" help=""> | 127 <param name="search_enzyme_cutafter" argument="-digest:search_enzyme_cutafter" type="text" optional="true" value="KR" label="Residues after which the enzyme cuts (specified as a string of amino acids)" help=""> |
| 128 <expand macro="list_string_san"/> | 128 <expand macro="list_string_san"/> |
| 224 <param name="add_R_arginine" argument="-statmod:add_R_arginine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to arginine" help=""/> | 224 <param name="add_R_arginine" argument="-statmod:add_R_arginine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to arginine" help=""/> |
| 225 <param name="add_Y_tyrosine" argument="-statmod:add_Y_tyrosine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tyrosine" help=""/> | 225 <param name="add_Y_tyrosine" argument="-statmod:add_Y_tyrosine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tyrosine" help=""/> |
| 226 <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/> | 226 <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/> |
| 227 </section> | 227 </section> |
| 228 <expand macro="adv_opts_macro"> | 228 <expand macro="adv_opts_macro"> |
| 229 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | 229 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
| 230 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 230 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
| 231 <expand macro="list_string_san"/> | 231 <expand macro="list_string_san"/> |
| 232 </param> | 232 </param> |
| 233 </expand> | 233 </expand> |
| 234 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | 234 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
| 235 <option value="opt_out_FLAG">opt_out (Statically add mass to tryptophan)</option> | 235 <option value="opt_out_FLAG">opt_out (MSFragger optional output file)</option> |
| 236 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 236 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
| 237 </param> | 237 </param> |
| 238 </inputs> | 238 </inputs> |
| 239 <outputs> | 239 <outputs> |
| 240 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> | 240 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> |
| 248 <tests> | 248 <tests> |
| 249 <expand macro="autotest_MSFraggerAdapter"/> | 249 <expand macro="autotest_MSFraggerAdapter"/> |
| 250 <expand macro="manutest_MSFraggerAdapter"/> | 250 <expand macro="manutest_MSFraggerAdapter"/> |
| 251 </tests> | 251 </tests> |
| 252 <help><![CDATA[Peptide Identification with MSFragger | 252 <help><![CDATA[Peptide Identification with MSFragger |
| 253 ]]></help> | 253 |
| 254 | |
| 255 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSFraggerAdapter.html]]></help> | |
| 254 <expand macro="references"/> | 256 <expand macro="references"/> |
| 255 </tool> | 257 </tool> |