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comparison idpqonvert.xml @ 21:e67c49262374 draft default tip

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author galaxyp
date Tue, 25 Jun 2013 17:07:34 -0400
parents 933a77287b5f
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20:5b790728e2e2 21:e67c49262374
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 -->