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comparison peptide_shaker.xml @ 12:8d2702c96689 draft

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author galaxyp
date Fri, 19 Jul 2013 11:20:56 -0400
parents 3e9201fe6785
children 6521f577059f
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11:3e9201fe6785 12:8d2702c96689
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" help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/> 91 <param format="fasta" name="input_database" type="data" label="Protein Database"/>
92 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" /> 92 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" />
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"> 93 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units">
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" help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> 97 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" />
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"/> 98 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" />
99 <param name="enzyme" type="select" label="Enzyme" help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> 99 <param name="enzyme" type="select" label="Enzyme">
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" help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/> 126 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" />
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"> 127 <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true">
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 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"> 133 <param name="variable_modifications" type="select" label="Variable Modification" multiple="true">
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" help="Lowest searched charge value for fragment ions"/> 139 <param name="min_charge" label="Minimum Charge" value="2" type="integer" />
140 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> 140 <param name="max_charge" label="Maximum Charge" value="4" type="integer" />
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"> 141 <param name="forward_ion" label="Forward Ion" type="select">
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" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> 146 <param name="reverse_ion" label="Reverse Ion" type="select">
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" help=" Run X! Tandem, OMSSA, or both and provide options for OMSSA search"/> 152 <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" />
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" 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 169 <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" />
170
171 .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" />
172 <when value="false" /> 170 <when value="false" />
173 <when value="true"> 171 <when value="true">
174 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> 172 <param name="protein_fdr" label="FDR at the protein 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" /> 173 <param name="peptide_fdr" label="FDR at the peptide 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" /> 174 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
184 </conditional> 182 </conditional>
185 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> 183 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
186 </when> 184 </when>
187 </conditional> 185 </conditional>
188 <conditional name="filtering_options"> 186 <conditional name="filtering_options">
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"/> 187 <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" />
190 <when value="false" /> 188 <when value="false" />
191 <when value="true"> 189 <when value="true">
192 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" /> 190 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
193 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" /> 191 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
194 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." /> 192 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />
213 <requirement type="package" version="1.14.1">SearchGUI</requirement> 211 <requirement type="package" version="1.14.1">SearchGUI</requirement>
214 </requirements> 212 </requirements>
215 <help> 213 <help>
216 **What it does** 214 **What it does**
217 215
218 Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results. 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.
219 217
220 ------ 218 ------
221 219
222 **Citation** 220 **Citation**
223 221