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comparison peptide_shaker.xml @ 0:0578e296cab4 draft

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Initial commit.
author galaxyp
date Fri, 10 May 2013 17:58:22 -0400
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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 mkdir spectra;
8 mkdir output;
9 mkdir output_reports;
10 cwd=`pwd`;
11 #for $mgf in $peak_lists:
12 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
13 ln -s '$mgf' 'spectra/$input_name';
14 #end for
15 SearchCLI \
16 -spectrum_files \$cwd/spectra \
17 -output_folder \$cwd/output \
18 -ppm $precursor_ion_tol_units \
19 -prec_tol $precursor_ion_tol \
20 -frag_tol $fragment_tol \
21 -enzyme '$enzyme' \
22 #set $fixed_mods_str = $fixed_modifications or ''
23 #set $variable_mods_str = $variable_modifications or ''
24 #if $fixed_mods_str
25 -fixed_mods "$fixed_mods_str" \
26 #end if
27 #if $variable_mods_str
28 -variable_mods "$variable_mods_str" \
29 #end if
30 -mc $missed_cleavages \
31 #if $advanced.specify:
32 -xtandem $advanced.xtandem \
33 #if $advanced.omssa.run_omssa
34 #set $omssa = 1
35 #else
36 #set $omssa = 0
37 #end if
38 -omssa $omssa \
39 #if $omssa == 1
40 -hitlist_length ${advanced.omssa.hitlist_length} \
41 -remove_prec ${advanced.omssa.remove_precursor} \
42 -scale_prec ${advanced.omssa.scale_precursor} \
43 -estimate_charge ${advanced.omssa.estimate_charge} \
44 #end if
45 #end if
46 -db $input_database;
47 PeptideShakerCLI \
48 -experiment 'Galaxy Experiment' \
49 -sample 'Sample' \
50 -replicate 1 \
51 -spectrum_files \$cwd/spectra \
52 -identification_files \$cwd/output \
53 -search_params \$cwd/output/SearchGUI.parameters \
54 -out_txt_1 \$cwd/output_reports \
55 #if $processing_options.specify
56 -protein_FDR ${processing_options.protein_fdr} \
57 -peptide_FDR ${processing_options.peptide_fdr} \
58 -psm_FDR ${processing_options.psm_fdr} \
59 -psm_FLR ${processing_options.psm_flr} \
60 #if str($processing_options.a_score.use) == "1"
61 #set $a_score = 1
62 #else
63 #set $a_score = 0
64 #end if
65 -a_score $a_score \
66 #if str($a_score) == "1"
67 -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \
68 #end if
69 #end if
70 #if $filtering_options.specify
71 -min_peptide_length ${filtering_options.min_peptide_length} \
72 -max_peptide_length ${filtering_options.max_peptide_length} \
73 -max_precursor_error ${filtering_options.max_precursor_error} \
74 -max_precursor_error_type ${filtering_options.max_precursor_error_type} \
75 -max_xtandem_e ${filtering_options.max_xtandem_e} \
76 -max_omssa_e ${filtering_options.max_omssa_e} \
77 -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \
78 #end if
79 -out \$cwd/output.cps ;
80 mv output_reports/*peptides.txt peptides.txt ;
81 mv output_reports/*psms.txt psms.txt ;
82 mv output_reports/*proteins.txt proteins.txt
83 </command>
84 <stdio>
85 <exit_code range="1:" level="fatal" description="Job Failed" />
86 </stdio>
87 <inputs>
88 <param format="fasta" name="input_database" type="data" label="Protein Database"/>
89 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" />
90 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units">
91 <option value="1">Parts per million (ppm)</option>
92 <option value="0">Daltons</option>
93 </param>
94 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" />
95 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" />
96 <param name="enzyme" type="select" label="Enzyme">
97 <option value="Trypsin">Trypsin</option>
98 <option value="Arg-C">Arg-C</option>
99 <option value="CNBr">CNBr</option>
100 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
101 <option value="Formic Acid">Formic Acid</option>
102 <option value="Lys-C">Lys-C</option>
103 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
104 <option value="Pepsin A">Pepsin A</option>
105 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
106 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
107 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
108 <option value="whole protein">whole protein</option>
109 <option value="Asp-N">Asp-N</option>
110 <option value="Glu-C">Glu-C</option>
111 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
112 <option value="Top-Down">Top-Down</option>
113 <option value="Semi-Tryptic">Semi-Tryptic</option>
114 <option value="No enzyme">No enzyme</option>
115 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
116 <option value="Asp-N (DE)">Asp-N (DE)</option>
117 <option value="Glu-C (DE)">Glu-C (DE)</option>
118 <option value="Lys-N (K)">Lys-N (K)</option>
119 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
120 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
121 <option value="Semi-Glu-C">Semi-Glu-C</option>
122 </param>
123 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" />
124 <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true">
125 <options from_file="searchgui_mods.loc">
126 <column name="name" index="0" />
127 <column name="value" index="0" />
128 </options>
129 </param>
130 <param name="variable_modifications" type="select" label="Variable Modification" multiple="true">
131 <options from_file="searchgui_mods.loc">
132 <column name="name" index="0" />
133 <column name="value" index="0" />
134 </options>
135 </param>
136 <param name="min_charge" label="Minimum Charge" value="2" type="integer" />
137 <param name="max_charge" label="Maximum Charge" value="4" type="integer" />
138 <param name="forward_ion" label="Forward Ion" type="select">
139 <option value="a">a</option>
140 <option value="b" selected="true">b</option>
141 <option value="c">c</option>
142 </param>
143 <param name="reverse_ion" label="Reverse Ion" type="select">
144 <option value="x">x</option>
145 <option value="y" selected="true">y</option>
146 <option value="z">z</option>
147 </param>
148 <conditional name="advanced">
149 <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" />
150 <when value="false" />
151 <when value="true">
152 <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" />
153 <conditional name="omssa">
154 <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" />
155 <when value="0" />
156 <when value="1">
157 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
158 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
159 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
160 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
161 </when>
162 </conditional>
163 </when>
164 </conditional>
165 <conditional name="processing_options">
166 <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" />
167 <when value="false" />
168 <when value="true">
169 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
170 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
171 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
172 <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" />
173 <conditional name="a_score">
174 <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" />
175 <when value="0" />
176 <when value="1">
177 <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
178 </when>
179 </conditional>
180 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
181 </when>
182 </conditional>
183 <conditional name="filtering_options">
184 <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" />
185 <when value="false" />
186 <when value="true">
187 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
188 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
189 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />
190 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
191 <option value="0">ppm</option>
192 <option value="1">Daltons</option>
193 </param>
194 <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" />
195 <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" />
196 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
197 </when>
198 </conditional>
199 </inputs>
200 <outputs>
201 <data format="cps" name="output" label="PeptideShaker CPS results for ${on_string}" from_work_dir="output.cps" />
202 <data format="tabular" name="output_peptides" label="PeptideShaker Peptide Report for ${on_string}" from_work_dir="peptides.txt" />
203 <data format="tabular" name="output_proteins" label="PeptideShaker Protein Report for ${on_string}" from_work_dir="proteins.txt" />
204 <data format="tabular" name="output_psms" label="PeptideShaker PSM Report for ${on_string}" from_work_dir="psms.txt" />
205 </outputs>
206 <requirements>
207 <requirement type="package">peptide_shaker</requirement>
208 <requirement type="package">searchgui</requirement>
209 </requirements>
210 <help>
211 **What it does**
212
213 ------
214
215 **Citation**
216
217 For the underlying tool, please cite `TODO`
218
219 If you use this tool in Galaxy, please cite TODO
220 </help>
221 </tool>