Mercurial > repos > galaxyp > peptideshaker
comparison peptide_shaker.xml @ 11:3e9201fe6785 draft
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author | galaxyp |
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date | Fri, 19 Jul 2013 11:06:52 -0400 |
parents | 74dbec22e775 |
children | 8d2702c96689 |
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10:74dbec22e775 | 11:3e9201fe6785 |
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86 </command> | 86 </command> |
87 <stdio> | 87 <stdio> |
88 <exit_code range="1:" level="fatal" description="Job Failed" /> | 88 <exit_code range="1:" level="fatal" description="Job Failed" /> |
89 </stdio> | 89 </stdio> |
90 <inputs> | 90 <inputs> |
91 <param format="fasta" name="input_database" type="data" label="Protein Database"/> | 91 <param format="fasta" name="input_database" type="data" label="Protein Database" help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/> |
92 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" /> | 92 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" /> |
93 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"> | 93 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> |
94 <option value="1">Parts per million (ppm)</option> | 94 <option value="1">Parts per million (ppm)</option> |
95 <option value="0">Daltons</option> | 95 <option value="0">Daltons</option> |
96 </param> | 96 </param> |
97 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" /> | 97 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> |
98 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" /> | 98 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" help="Provide error value for fragment ions, based on instrument used"/> |
99 <param name="enzyme" type="select" label="Enzyme"> | 99 <param name="enzyme" type="select" label="Enzyme" help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> |
100 <option value="Trypsin">Trypsin</option> | 100 <option value="Trypsin">Trypsin</option> |
101 <option value="Arg-C">Arg-C</option> | 101 <option value="Arg-C">Arg-C</option> |
102 <option value="CNBr">CNBr</option> | 102 <option value="CNBr">CNBr</option> |
103 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> | 103 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> |
104 <option value="Formic Acid">Formic Acid</option> | 104 <option value="Formic Acid">Formic Acid</option> |
121 <option value="Lys-N (K)">Lys-N (K)</option> | 121 <option value="Lys-N (K)">Lys-N (K)</option> |
122 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> | 122 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> |
123 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> | 123 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> |
124 <option value="Semi-Glu-C">Semi-Glu-C</option> | 124 <option value="Semi-Glu-C">Semi-Glu-C</option> |
125 </param> | 125 </param> |
126 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" /> | 126 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/> |
127 <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true"> | 127 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> |
128 <options from_file="searchgui_mods.loc"> | 128 <options from_file="searchgui_mods.loc"> |
129 <column name="name" index="0" /> | 129 <column name="name" index="0" /> |
130 <column name="value" index="0" /> | 130 <column name="value" index="0" /> |
131 </options> | 131 </options> |
132 </param> | 132 </param> |
133 <param name="variable_modifications" type="select" label="Variable Modification" multiple="true"> | 133 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> |
134 <options from_file="searchgui_mods.loc"> | 134 <options from_file="searchgui_mods.loc"> |
135 <column name="name" index="0" /> | 135 <column name="name" index="0" /> |
136 <column name="value" index="0" /> | 136 <column name="value" index="0" /> |
137 </options> | 137 </options> |
138 </param> | 138 </param> |
139 <param name="min_charge" label="Minimum Charge" value="2" type="integer" /> | 139 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> |
140 <param name="max_charge" label="Maximum Charge" value="4" type="integer" /> | 140 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> |
141 <param name="forward_ion" label="Forward Ion" type="select"> | 141 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> |
142 <option value="a">a</option> | 142 <option value="a">a</option> |
143 <option value="b" selected="true">b</option> | 143 <option value="b" selected="true">b</option> |
144 <option value="c">c</option> | 144 <option value="c">c</option> |
145 </param> | 145 </param> |
146 <param name="reverse_ion" label="Reverse Ion" type="select"> | 146 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> |
147 <option value="x">x</option> | 147 <option value="x">x</option> |
148 <option value="y" selected="true">y</option> | 148 <option value="y" selected="true">y</option> |
149 <option value="z">z</option> | 149 <option value="z">z</option> |
150 </param> | 150 </param> |
151 <conditional name="advanced"> | 151 <conditional name="advanced"> |
152 <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" /> | 152 <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" help=" Run X! Tandem, OMSSA, or both and provide options for OMSSA search"/> |
153 <when value="false" /> | 153 <when value="false" /> |
154 <when value="true"> | 154 <when value="true"> |
155 <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" /> | 155 <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
156 <conditional name="omssa"> | 156 <conditional name="omssa"> |
157 <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" /> | 157 <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
164 </when> | 164 </when> |
165 </conditional> | 165 </conditional> |
166 </when> | 166 </when> |
167 </conditional> | 167 </conditional> |
168 <conditional name="processing_options"> | 168 <conditional name="processing_options"> |
169 <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" /> | 169 <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" help="Select and provide False Discovery Rate (FDR) levels at the peptide, protein, and peptide-spectral match (PSM) levels, as well as False Loss Rate (FLR) for PSM’s and A score options for post-translational modifications (PTM’s). See this link_ for more details |
170 | |
171 .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" /> | |
170 <when value="false" /> | 172 <when value="false" /> |
171 <when value="true"> | 173 <when value="true"> |
172 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> | 174 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> |
173 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> | 175 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> |
174 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> | 176 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> |
182 </conditional> | 184 </conditional> |
183 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> | 185 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> |
184 </when> | 186 </when> |
185 </conditional> | 187 </conditional> |
186 <conditional name="filtering_options"> | 188 <conditional name="filtering_options"> |
187 <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" /> | 189 <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"/> |
188 <when value="false" /> | 190 <when value="false" /> |
189 <when value="true"> | 191 <when value="true"> |
190 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" /> | 192 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" /> |
191 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" /> | 193 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" /> |
192 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." /> | 194 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." /> |
211 <requirement type="package" version="1.14.1">SearchGUI</requirement> | 213 <requirement type="package" version="1.14.1">SearchGUI</requirement> |
212 </requirements> | 214 </requirements> |
213 <help> | 215 <help> |
214 **What it does** | 216 **What it does** |
215 | 217 |
216 Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the result via PeptideShaker. | 218 Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results. |
217 | 219 |
218 ------ | 220 ------ |
219 | 221 |
220 **Citation** | 222 **Citation** |
221 | 223 |