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comparison peptide_shaker.xml @ 13:6521f577059f draft

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author galaxyp
date Fri, 19 Jul 2013 11:32:58 -0400
parents 8d2702c96689
children db6cc184146c
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12:8d2702c96689 13:6521f577059f
1 <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">
2 <!-- TODO: Set defaults for weights correctly -->
3 <description>
4 Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
5 </description>
6 <command>
7 #from datetime import datetime
8 #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s")
9 #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s")
10 mkdir spectra;
11 mkdir output;
12 mkdir output_reports;
13 cwd=`pwd`;
14 #for $mgf in $peak_lists:
15 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
16 ln -s '$mgf' 'spectra/$input_name';
17 #end for
18 SearchCLI \
19 -spectrum_files \$cwd/spectra \
20 -output_folder \$cwd/output \
21 -ppm $precursor_ion_tol_units \
22 -prec_tol $precursor_ion_tol \
23 -frag_tol $fragment_tol \
24 -enzyme '$enzyme' \
25 #set $fixed_mods_str = $fixed_modifications or ''
26 #set $variable_mods_str = $variable_modifications or ''
27 #if $fixed_mods_str
28 -fixed_mods "$fixed_mods_str" \
29 #end if
30 #if $variable_mods_str
31 -variable_mods "$variable_mods_str" \
32 #end if
33 -mc $missed_cleavages \
34 #if $advanced.specify:
35 -xtandem $advanced.xtandem \
36 #if $advanced.omssa.run_omssa
37 #set $omssa = 1
38 #else
39 #set $omssa = 0
40 #end if
41 -omssa $omssa \
42 #if $omssa == 1
43 -hitlist_length ${advanced.omssa.hitlist_length} \
44 -remove_prec ${advanced.omssa.remove_precursor} \
45 -scale_prec ${advanced.omssa.scale_precursor} \
46 -estimate_charge ${advanced.omssa.estimate_charge} \
47 #end if
48 #end if
49 -db $input_database;
50 PeptideShakerCLI \
51 -experiment '$exp_str' \
52 -sample '$samp_str' \
53 -replicate 1 \
54 -spectrum_files \$cwd/spectra \
55 -identification_files \$cwd/output \
56 -search_params \$cwd/output/SearchGUI.parameters \
57 -out_txt_1 \$cwd/output_reports \
58 #if $processing_options.specify
59 -protein_FDR ${processing_options.protein_fdr} \
60 -peptide_FDR ${processing_options.peptide_fdr} \
61 -psm_FDR ${processing_options.psm_fdr} \
62 -psm_FLR ${processing_options.psm_flr} \
63 #if str($processing_options.a_score.use) == "1"
64 #set $a_score = 1
65 #else
66 #set $a_score = 0
67 #end if
68 -a_score $a_score \
69 #if str($a_score) == "1"
70 -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \
71 #end if
72 #end if
73 #if $filtering_options.specify
74 -min_peptide_length ${filtering_options.min_peptide_length} \
75 -max_peptide_length ${filtering_options.max_peptide_length} \
76 -max_precursor_error ${filtering_options.max_precursor_error} \
77 -max_precursor_error_type ${filtering_options.max_precursor_error_type} \
78 -max_xtandem_e ${filtering_options.max_xtandem_e} \
79 -max_omssa_e ${filtering_options.max_omssa_e} \
80 -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \
81 #end if
82 -out \$cwd/output.cps ;
83 mv output_reports/*peptides.txt peptides.txt ;
84 mv output_reports/*psms.txt psms.txt ;
85 mv output_reports/*proteins.txt proteins.txt
86 </command>
87 <stdio>
88 <exit_code range="1:" level="fatal" description="Job Failed" />
89 </stdio>
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"/>
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" 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>
95 <option value="0">Daltons</option>
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"/>
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" help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
100 <option value="Trypsin">Trypsin</option>
101 <option value="Arg-C">Arg-C</option>
102 <option value="CNBr">CNBr</option>
103 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
104 <option value="Formic Acid">Formic Acid</option>
105 <option value="Lys-C">Lys-C</option>
106 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
107 <option value="Pepsin A">Pepsin A</option>
108 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
109 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
110 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
111 <option value="whole protein">whole protein</option>
112 <option value="Asp-N">Asp-N</option>
113 <option value="Glu-C">Glu-C</option>
114 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
115 <option value="Top-Down">Top-Down</option>
116 <option value="Semi-Tryptic">Semi-Tryptic</option>
117 <option value="No enzyme">No enzyme</option>
118 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
119 <option value="Asp-N (DE)">Asp-N (DE)</option>
120 <option value="Glu-C (DE)">Glu-C (DE)</option>
121 <option value="Lys-N (K)">Lys-N (K)</option>
122 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
123 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
124 <option value="Semi-Glu-C">Semi-Glu-C</option>
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"/>
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">
129 <column name="name" index="0" />
130 <column name="value" index="0" />
131 </options>
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">
134 <options from_file="searchgui_mods.loc">
135 <column name="name" index="0" />
136 <column name="value" index="0" />
137 </options>
138 </param>
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" help="Highest searched charge value for fragment ions"/>
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>
143 <option value="b" selected="true">b</option>
144 <option value="c">c</option>
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">
147 <option value="x">x</option>
148 <option value="y" selected="true">y</option>
149 <option value="z">z</option>
150 </param>
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"/>
153 <when value="false" />
154 <when value="true">
155 <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" />
156 <conditional name="omssa">
157 <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" />
158 <when value="0" />
159 <when value="1">
160 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
161 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
162 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
163 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
164 </when>
165 </conditional>
166 </when>
167 </conditional>
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
170
171 .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" />
172 <when value="false" />
173 <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" />
175 <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" />
177 <param name="psm_flr" label="FLR at the PSM level" help="In percent (default 1% FLR: '1'). Percent for peptides with different potential modification sites and one variable modification." value="1" type="float" />
178 <conditional name="a_score">
179 <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" />
180 <when value="0" />
181 <when value="1">
182 <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
183 </when>
184 </conditional>
185 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
186 </when>
187 </conditional>
188 <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"/>
190 <when value="false" />
191 <when value="true">
192 <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" />
194 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />
195 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
196 <option value="0">ppm</option>
197 <option value="1">Daltons</option>
198 </param>
199 <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" />
200 <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" />
201 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
202 </when>
203 </conditional>
204 </inputs>
205 <outputs>
206 <data format="cps" name="output" label="PeptideShaker CPS results for ${on_string}" from_work_dir="output.cps" />
207 <data format="tabular" name="output_peptides" label="PeptideShaker Peptide Report for ${on_string}" from_work_dir="peptides.txt" />
208 <data format="tabular" name="output_proteins" label="PeptideShaker Protein Report for ${on_string}" from_work_dir="proteins.txt" />
209 <data format="tabular" name="output_psms" label="PeptideShaker PSM Report for ${on_string}" from_work_dir="psms.txt" />
210 </outputs>
211 <requirements>
212 <requirement type="package" version="0.20.1">PeptideShaker</requirement>
213 <requirement type="package" version="1.14.1">SearchGUI</requirement>
214 </requirements>
215 <help>
216 **What it does**
217
218 Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.
219
220 ------
221
222 **Citation**
223
224 For the underlying tool, please cite `TODO`
225
226 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker
227 </help>
228 </tool>
1 <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0"> 229 <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">
2 <!-- TODO: Set defaults for weights correctly --> 230 <!-- TODO: Set defaults for weights correctly -->
3 <description> 231 <description>
4 Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. 232 Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
5 </description> 233 </description>