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comparison peptide_shaker.xml @ 11:3e9201fe6785 draft

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author galaxyp
date Fri, 19 Jul 2013 11:06:52 -0400
parents 74dbec22e775
children 8d2702c96689
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10:74dbec22e775 11:3e9201fe6785
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