Mercurial > repos > galaxyp > openms_msfraggeradapter

comparison MSFraggerAdapter.xml @ 2:6bcc338b9dc6 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 20:09:43 +0000
parents 5a9c3e827da5
children e133b5c8878f
comparison
equal deleted inserted replaced
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>