|
19
|
1 <tool id="idpQonvert" name="idpQonvert" version="0.1.0">
|
|
|
2 <!-- TODO: Set defaults for weights correctly -->
|
|
|
3 <description>
|
|
|
4 Prepare identification results for IDPicker.
|
|
|
5 </description>
|
|
|
6 <command>
|
|
|
7 #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
|
|
|
8 #set $input_name = $input.display_name
|
|
|
9 #set $output_name = $input_name.split(".")[0] + ".idpDB"
|
|
|
10 ln -s '$input' '${input_name}';
|
|
|
11 ln -s '$input_database' '${db_name}';
|
|
|
12 idpQonvert -DecoyPrefix '${decoy_prefix}' \
|
|
|
13 -WriteQonversionDetails true \
|
|
|
14 -ProteinDatabase '${db_name}' \
|
|
|
15 -MaxFDR $max_fdr \
|
|
|
16 -EmbedSpectrumScanTimes false \
|
|
|
17 -EmbedSpectrumSources false \
|
|
|
18 #if $scoring.override_scoring
|
|
|
19 #set $score_info = []
|
|
|
20 #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:spacevalue"]
|
|
|
21 #set $weight = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_weight.value")
|
|
|
22 #set $type = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_type.value")
|
|
|
23 #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
|
|
|
24 #continue
|
|
|
25 #end for
|
|
|
26 #set $score_str = "; ".join($score_info)
|
|
|
27 -ScoreInfo '$score_str' \
|
|
|
28 #end if
|
|
|
29 #if $advanced_options.use_advanced_options
|
|
|
30 -MaxImportFDR $advanced_options.max_import_fdr \
|
|
|
31 -MaxResultRank $advanced_options.max_result_rank \
|
|
|
32 -RerankMatches $advanced_options.rerank_matches \
|
|
|
33 -Gamma $advanced_options.gamma \
|
|
|
34 -Nu $advanced_options.nu \
|
|
|
35 -PolynomialDegree $advanced_options.polynomial_degree \
|
|
|
36 -TruePositiveThreshold $advanced_options.true_positive_threshold \
|
|
|
37 -MaxTrainingRank $advanced_options.max_training_rank \
|
|
|
38 -SVMType $advanced_options.svm_type \
|
|
|
39 -Kernel $advanced_options.kernel \
|
|
|
40 -ChargeStateHandling $advanced_options.charge_state_handling \
|
|
|
41 -QonverterMethod $advanced_options.qonverter_method \
|
|
|
42 -MinPartitionSize $advanced_options.min_partition_size \
|
|
|
43 #end if
|
|
|
44 '${input_name}';
|
|
|
45 mv '$output_name' output
|
|
|
46 </command>
|
|
|
47 <!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
|
|
|
48 -->
|
|
|
49 <stdio>
|
|
|
50 <exit_code range="1:" level="fatal" description="Job Failed" />
|
|
|
51 <regex match="^Could not find the default configuration file.*$"
|
|
|
52 source="both"
|
|
|
53 level="warning" />
|
|
|
54 </stdio>
|
|
|
55 <inputs>
|
|
|
56 <conditional name="type">
|
|
|
57 <param name="input_type" type="select" label="Input Type">
|
|
|
58 <option value="mzid">mzIdentML</option>
|
|
|
59 <option value="pepXML">pepXML</option>
|
|
|
60 </param>
|
|
|
61 <when value="mzid">
|
|
|
62 <param format="mzid" name="input" type="data" label="Input mzIdentML"/>
|
|
|
63 </when>
|
|
|
64 <when value="pepXML">
|
|
|
65 <param format="pepXML" name="input" type="data" label="Input pepXML"/>
|
|
|
66 </when>
|
|
|
67 </conditional>
|
|
|
68 <param format="fasta" name="input_database" type="data" label="Protein Database"/>
|
|
|
69 <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
|
|
|
70 <param name="max_fdr" type="float" label="Max FDR" value="0.05" />
|
|
|
71 <conditional name="advanced_options">
|
|
|
72 <param name="use_advanced_options" type="boolean" truevalue="true" falsevalue="false" label="Set Advanced Options" help="" />
|
|
|
73 <when value="false" />
|
|
|
74 <when value="true">
|
|
|
75 <param name="max_import_fdr" type="float" label="Max Import FDR" value="0.25" />
|
|
|
76 <param name="max_result_rank" type="integer" label="Max Result Rank" value="3" />
|
|
|
77 <param name="max_training_rank" type="integer" label="Max Training Rank" value="1" />
|
|
|
78 <param name="rerank_matches" type="boolean" label="Rerank Matches" checked="false" truevalue="true" falsevalue="false" />
|
|
|
79 <param name="gamma" type="float" label="Gamma" value="5" />
|
|
|
80 <param name="nu" type="float" label="Nu" value="-0.5" />
|
|
|
81 <param name="true_positive_threshold" type="float" label="True Positive Threshold" value="0.01" />
|
|
|
82 <param name="polynomial_degree" type="integer" label="Polynomial Degree" value="3" />
|
|
|
83 <param name="min_partition_size" type="integer" label="Minimum Partition Size" value="10" />
|
|
|
84 <param name="svm_type" label="SVM Type" type="select">
|
|
|
85 <option value="CSVC" selected="true">CSVC</option>
|
|
|
86 <option value="NuSVC">Nu SCV</option>
|
|
|
87 <option value="OneClass">One Class</option>
|
|
|
88 <option value="NuSVR">Nu SVR</option>
|
|
|
89 <option value="EpsilonSVR">Epsilon SVR</option>
|
|
|
90 </param>
|
|
|
91 <param name="kernel" label="Kernel" type="select">
|
|
|
92 <option value="Linear" selected="true">Linear</option>
|
|
|
93 <option value="Polynomial">Polynomial</option>
|
|
|
94 <option value="RBR">Radial Basis Function</option>
|
|
|
95 <option value="Sigmoid">Sigmoid</option>
|
|
|
96 </param>
|
|
|
97 <param name="charge_state_handling" label="Charge State Handling" type="select">
|
|
|
98 <option value="Partition" selected="true">Partition</option>
|
|
|
99 <option value="Ignore">Ignore</option>
|
|
|
100 <option value="Feature">Feature</option>
|
|
|
101 </param>
|
|
|
102 <param name="terminal_specificity_handling" label="Terminal Specificity Handling" type="select">
|
|
|
103 <option value="Partition" selected="true">Partition</option>
|
|
|
104 <option value="Ignore">Ignore</option>
|
|
|
105 <option value="Feature">Feature</option>
|
|
|
106 </param>
|
|
|
107 <param name="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
|
|
|
108 <option value="Ignore" selected="true">Ignore</option>
|
|
|
109 <option value="Feature">Feature</option>
|
|
|
110 </param>
|
|
|
111 <param name="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
|
|
|
112 <option value="Ignore" selected="true">Ignore</option>
|
|
|
113 <option value="Feature">Feature</option>
|
|
|
114 </param>
|
|
|
115 <param name="mass_error_handling" label="Mass Error Handling" type="select">
|
|
|
116 <option value="Ignore" selected="true">Ignore</option>
|
|
|
117 <option value="Feature">Feature</option>
|
|
|
118 </param>
|
|
|
119 <param name="qonverter_method" label="Qonverter Method" type="select">
|
|
|
120 <option value="MonteCarlo" selected="true">Monte Carlo</option>
|
|
|
121 <option value="SingleSVM">SVM (single)</option>
|
|
|
122 <option value="PartitionSVM">SVM (parition)</option>
|
|
|
123 <option value="StaticWeighted">Static Weighted</option>
|
|
|
124 </param>
|
|
|
125 </when>
|
|
|
126 </conditional>
|
|
|
127 <conditional name="scoring">
|
|
|
128 <param name="override_scoring" type="boolean" truevalue="true" falsevalue="false" label="Modify Search Application Weights" />
|
|
|
129 <when value="false" />
|
|
|
130 <when value="true">
|
|
|
131 <param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" value="1" />
|
|
|
132 <param name="myrimatch_mvh_type" label="Myrimatch (mvh) Normalization" type="select">
|
|
|
133 <option value="off" selected="true">None</option>
|
|
|
134 <option value="quantile">Quantile</option>
|
|
|
135 <option value="linear">Linear</option>
|
|
|
136 </param>
|
|
|
137 <param name="xcorr_weight" label="XCorr Weight" type="float" value="1" />
|
|
|
138 <param name="xcorr_type" label="XCorr Normalization" type="select">
|
|
|
139 <option value="off" selected="true">None</option>
|
|
|
140 <option value="quantile">Quantile</option>
|
|
|
141 <option value="linear">Linear</option>
|
|
|
142 </param>
|
|
|
143 <param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" value="1" />
|
|
|
144 <param name="sequest_xcorr_type" label="Sequest (xcorr) Normalization" type="select">
|
|
|
145 <option value="off" selected="true">None</option>
|
|
|
146 <option value="quantile">Quantile</option>
|
|
|
147 <option value="linear">Linear</option>
|
|
|
148 </param>
|
|
|
149 <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" value="1" />
|
|
|
150 <param name="sequest_deltacn_type" label="Sequest (deltacn) Normalization" type="select">
|
|
|
151 <option value="off" selected="true">None</option>
|
|
|
152 <option value="quantile">Quantile</option>
|
|
|
153 <option value="linear">Linear</option>
|
|
|
154 </param>
|
|
|
155 <param name="mascot_score_weight" label="Mascot Score Weight" type="float" value="1" />
|
|
|
156 <param name="mascot_score_type" label="Mascot Score Normalization" type="select">
|
|
|
157 <option value="off" selected="true">None</option>
|
|
|
158 <option value="quantile">Quantile</option>
|
|
|
159 <option value="linear">Linear</option>
|
|
|
160 </param>
|
|
|
161 <param name="xtandem_expect_weight" label="X! Tandem (Expectation) Weight" type="float" value="-1" />
|
|
|
162 <param name="xtandem_expect_type" label="X! Tandem (Expectation) Normalization" type="select">
|
|
|
163 <option value="off" selected="true">None</option>
|
|
|
164 <option value="quantile">Quantile</option>
|
|
|
165 <option value="linear">Linear</option>
|
|
|
166 </param>
|
|
|
167 <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" value="1" />
|
|
|
168 <param name="xtandem_hyperscore_type" label="X! Tandem (hyperscore)Normalization" type="select">
|
|
|
169 <option value="off" selected="true">None</option>
|
|
|
170 <option value="quantile">Quantile</option>
|
|
|
171 <option value="linear">Linear</option>
|
|
|
172 </param>
|
|
|
173 <param name="ms-gf_spacevalue_weight" label="MS-GF (spacevalue) Weight" type="float" value="-1" />
|
|
|
174 <param name="ms-gf_spacevalue_type" label="MS-GF (spacevalue) Normalization" type="select">
|
|
|
175 <option value="off" selected="true">None</option>
|
|
|
176 <option value="quantile">Quantile</option>
|
|
|
177 <option value="linear">Linear</option>
|
|
|
178 </param>
|
|
|
179 </when>
|
|
|
180 </conditional>
|
|
|
181 </inputs>
|
|
|
182 <outputs>
|
|
|
183 <data format="idpdb" name="output" from_work_dir="output" />
|
|
|
184 </outputs>
|
|
|
185 <requirements>
|
|
|
186 <requirement type="package" version="3.0.475">idpQonvert</requirement>
|
|
|
187 </requirements>
|
|
|
188 <help>
|
|
|
189 **What it does**
|
|
|
190
|
|
|
191 ------
|
|
|
192
|
|
|
193 **Citation**
|
|
|
194
|
|
|
195 For the underlying tool, please cite `TODO`
|
|
|
196
|
|
|
197 If you use this tool in Galaxy, please cite TODO
|
|
|
198 </help>
|
|
|
199 </tool>
|
|
|
200 <!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
|
|
|
201
|
|
|
202 idpQonvert -OverwriteExistingFiles true -MaxFDR 0.05 -MaxImportFDR 0.25 -MaxResultRank 3 -RerankMatches false -TruePositiveThreshold 0.01 -MaxTrainingRank 1 -Gamma 5 -Nu -0.5 -PolynomialDegree 3 -ScoreInfo "1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off xexpect; 1 off x\!tandem:hyperscore; -1 off ms-gf:specevalue" -SVMType CSVC -Kernel Linear -ChargeStateHandling Partition -QonverterMethod MonteCarlo -MinPartitionSize 10 -DecoyPrefix RRRRRR -ProteinDatabase test2.fasta input.pepXML
|
|
|
203
|
|
|
204
|
|
|
205 ScoreInfo: 1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off x!tandem:expect; 1 off x!tandem:hyperscore; -1 off ms-gf:specevalue
|
|
|
206
|
|
|
207 off is normalization: quantile, linear, or off
|
|
|
208
|
|
|
209 SVMType: CSVC, NuSVC, OneClass, EpsilonSVR, NuSVR
|
|
|
210 Kernel: Linear, Polynomial, RBF (radial basis function), Sigmoid
|
|
|
211 ChargeStateHandling: Parition, Ignore, Feature
|
|
|
212 TerminalSpecificityHandling: Partition, Ignore, Feature
|
|
|
213 MissedCleavagesHandling: Ignore, Feature
|
|
|
214 MassErrorHandling: Ignore, Feature
|
|
|
215 QonverterMethod: MonteCarlo, SingleSVM, PartitionedSVM, StaticWeighted
|
|
|
216
|
|
|
217 -->
|
