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comparison idpqonvert.xml @ 3:d1f7b2395bc2 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
author galaxyp
date Thu, 15 Dec 2016 17:20:57 -0500
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children feebe32c3a52
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2:e39c5664b04a 3:d1f7b2395bc2
1 <?xml version="1.0"?>
2 <tool id="idpqonvert" name="idpQonvert" version="@VERSION@.0">
3 <description>Prepare identification results for IDPicker</description>
4 <macros>
5 <import>macros.xml</import>
6 <xml name="normalizationOptions">
7 <option value="off" selected="true">None</option>
8 <option value="quantile">Quantile</option>
9 <option value="linear">Linear</option>
10 </xml>
11 </macros>
12 <expand macro="requirements" />
13 <stdio>
14 <exit_code range="1:" level="fatal" description="Job Failed" />
15 <regex match="^Error:.*$" source="both" level="fatal" />
16 </stdio>
17 <command>
18 <![CDATA[
19 #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta"
20 #set $input_name = $input.display_name
21 #set $output_name = $input_name.split(".")[0] + ".idpDB"
22 ln -s '$input' '${input_name}' &&
23 ln -s '$ProteinDatabase' '${db_name}' &&
24
25 idpQonvert
26 -DecoyPrefix '${DecoyPrefix}'
27 -WriteQonversionDetails true
28 -ProteinDatabase '${db_name}'
29 -MaxFDR $MaxFDR
30 -EmbedSpectrumScanTimes false
31 -EmbedSpectrumSources false
32 #set $score_info = []
33 #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:specevalue", "comet:xcorr", "comet:deltacn", "comet:expect"]
34 #set $name = $engine.replace(":", "_").replace("!","")
35 #set $weight = $getVar("scoring." + $name + "." + $name + "_weight.value")
36 #set $type = $getVar("scoring." + $name + "." + $name + "_type.value")
37 #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
38 #continue
39 #end for
40 #for $i, $s in enumerate($scoring.extra_score)
41 #set $name = $s.extra_score_name
42 #set $type = $s.extra_score_normalization
43 #set $weight = $s.extra_score_weight
44 #set $score_info = $score_info + [str($weight) + " " + $type + " " + $name]
45 #end for
46 #set $score_str = "; ".join($score_info)
47 -ScoreInfo '$score_str'
48 -MaxImportFDR $advanced_options.MaxImportFDR
49 -MaxResultRank $advanced_options.MaxResultRank
50 -RerankMatches $advanced_options.RerankMatches
51 -Gamma $advanced_options.Gamma
52 -Nu $advanced_options.Nu
53 -PolynomialDegree $advanced_options.PolynomialDegree
54 -TruePositiveThreshold $advanced_options.TruePositiveThreshold
55 -MaxTrainingRank $advanced_options.MaxTrainingRank
56 -SVMType $advanced_options.SVMType
57 -Kernel $advanced_options.Kernel
58 -ChargeStateHandling $advanced_options.ChargeStateHandling
59 -TerminalSpecificityHandling $advanced_options.TerminalSpecificityHandling
60 -MissedCleavagesHandling $advanced_options.MissedCleavagesHandling
61 -QonverterMethod $advanced_options.QonverterMethod
62 -MinPartitionSize $advanced_options.MinPartitionSize
63 '${input_name}' &&
64 mv '$output_name' output
65 ]]>
66 </command>
67 <inputs>
68 <param name="input" type="data" format="mzid,raw_pepxml" label="Input mzIdentML/pepXML file(s)" />
69 <param argument="-ProteinDatabase" format="fasta" type="data" label="Protein Database" help="The FASTA protein database to map peptides against. Only peptides from target proteins will be mapped; decoy peptides will be stored as-is in the idpDB." />
70 <param argument="-DecoyPrefix" type="text" label="Decoy Prefix" help="The prefix to look for on protein accessions to determine whether it is a target or decoy." />
71 <param argument="-MaxFDR" type="float" label="Max FDR" min="0.0000001" value="0.05" help="PSMs with a greater FDR than this will be excluded from the filtered data set, but remain in the file." />
72 <section name="advanced_options" title="Advanced Options">
73 <param argument="-MaxImportFDR" type="float" label="Max Import FDR" min="0.1" value="0.25" help="PSMs with a greater FDR than this will be completely excluded from the idpDB." />
74 <param argument="-MaxResultRank" type="integer" label="Max Result Rank" min="1" value="2" />
75 <param argument="-MaxTrainingRank" type="integer" label="Max Training Rank" min="1" value="1" />
76 <param argument="-RerankMatches" type="boolean" label="Rerank Matches" checked="false" truevalue="true" falsevalue="false" />
77 <param argument="-Gamma" type="float" label="Gamma" value="5" />
78 <param argument="-Nu" type="float" label="Nu" value="-0.5" />
79 <param argument="-TruePositiveThreshold" type="float" label="True Positive Threshold" min="0.0000001" value="0.01" />
80 <param argument="-PolynomialDegree" type="integer" label="Polynomial Degree" min="1" value="3" />
81 <param argument="-MinPartitionSize" type="integer" label="Minimum Partition Size" min="10" value="10" />
82 <param argument="-SVMType" label="SVM Type" type="select">
83 <option value="CSVC" selected="true">CSVC</option>
84 <option value="NuSVC">Nu SCV</option>
85 <option value="OneClass">One Class</option>
86 <option value="NuSVR">Nu SVR</option>
87 <option value="EpsilonSVR">Epsilon SVR</option>
88 </param>
89 <param argument="-Kernel" label="Kernel" type="select">
90 <option value="Linear" selected="true">Linear</option>
91 <option value="Polynomial">Polynomial</option>
92 <option value="RBR">Radial Basis Function</option>
93 <option value="Sigmoid">Sigmoid</option>
94 </param>
95 <param argument="-ChargeStateHandling" label="Charge State Handling" type="select">
96 <option value="Partition" selected="true">Partition</option>
97 <option value="Ignore">Ignore</option>
98 <option value="Feature">Feature</option>
99 </param>
100 <param argument="-TerminalSpecificityHandling" label="Terminal Specificity Handling" type="select">
101 <option value="Partition" selected="true">Partition</option>
102 <option value="Ignore">Ignore</option>
103 <option value="Feature">Feature</option>
104 </param>
105 <param argument="-MissedCleavagesHandling" label="Missed Cleavages Handling" type="select">
106 <option value="Ignore" selected="true">Ignore</option>
107 <option value="Feature">Feature</option>
108 </param>
109 <param argument="-MassErrorHandling" label="Mass Error Handling" type="select">
110 <option value="Ignore" selected="true">Ignore</option>
111 <option value="Feature">Feature</option>
112 </param>
113 <param argument="-QonverterMethod" label="Qonverter Method" type="select">
114 <option value="MonteCarlo" selected="true">Monte Carlo (recommended)</option>
115 <option value="SingleSVM">SVM (single)</option>
116 <option value="PartitionSVM">SVM (parition)</option>
117 <option value="StaticWeighted">Static Weighted</option>
118 </param>
119 </section>
120 <section name="scoring" title="Custom Score Settings">
121 <section name="myrimatch_mvh" title="Myrimatch (mvh) Score/Weight" expanded="False">
122 <param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" min="-1" max="1" value="1" />
123 <param name="myrimatch_mvh_type" label="Myrimatch (mvh) Normalization" type="select"><expand macro="normalizationOptions" /></param>
124 </section>
125 <section name="xcorr" title="Non-Sequest (xcorr) Score/Weight" expanded="False">
126 <param name="xcorr_weight" label="XCorr Weight" type="float" min="-1" max="1" value="1" />
127 <param name="xcorr_type" label="XCorr Normalization" type="select"><expand macro="normalizationOptions" /></param>
128 </section>
129 <section name="sequest_xcorr" title="Sequest (xcorr) Score/Weight" expanded="False">
130 <param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" min="-1" max="1" value="1" />
131 <param name="sequest_xcorr_type" label="Sequest (xcorr) Normalization" type="select"><expand macro="normalizationOptions" /></param>
132 </section>
133 <section name="sequest_deltacn" title="Sequest (deltacn) Score/Weight" expanded="False">
134 <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" min="-1" max="1" value="1" />
135 <param name="sequest_deltacn_type" label="Sequest (deltacn) Normalization" type="select"><expand macro="normalizationOptions" /></param>
136 </section>
137 <section name="mascot_score" title="Mascot (score) Score/Weight" expanded="False">
138 <param name="mascot_score_weight" label="Mascot Score Weight" type="float" min="-1" max="1" value="1" />
139 <param name="mascot_score_type" label="Mascot Score Normalization" type="select"><expand macro="normalizationOptions" /></param>
140 </section>
141 <section name="xtandem_expect" title="X! Tandem (expect) Score/Weight" expanded="False">
142 <param name="xtandem_expect_weight" label="X! Tandem (expectation) Weight" type="float" min="-1" max="1" value="-1" />
143 <param name="xtandem_expect_type" label="X! Tandem (expectation) Normalization" type="select"><expand macro="normalizationOptions" /></param>
144 </section>
145 <section name="xtandem_hyperscore" title="X! Tandem (hyperscore) Score/Weight" expanded="False">
146 <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" min="-1" max="1" value="1" />
147 <param name="xtandem_hyperscore_type" label="X! Tandem (hyperscore)Normalization" type="select"><expand macro="normalizationOptions" /></param>
148 </section>
149 <section name="ms-gf_specevalue" title="MS-GF+ (specevalue) Score/Weight" expanded="False">
150 <param name="ms-gf_specevalue_weight" label="MS-GF+ (specevalue) Weight" type="float" min="-1" max="1" value="-1" />
151 <param name="ms-gf_specevalue_type" label="MS-GF+ (specevalue) Normalization" type="select"><expand macro="normalizationOptions" /></param>
152 </section>
153 <section name="comet_xcorr" title="Comet (xcorr) Score/Weight" expanded="False">
154 <param name="comet_xcorr_weight" label="Comet (xcorr) Weight" type="float" min="-1" max="1" value="1" />
155 <param name="comet_xcorr_type" label="Comet (xcorr) Normalization" type="select"><expand macro="normalizationOptions" /></param>
156 </section>
157 <section name="comet_deltacn" title="Comet (deltacn) Score/Weight" expanded="False">
158 <param name="comet_deltacn_weight" label="Comet (deltacn) Weight" type="float" min="-1" max="1" value="1" />
159 <param name="comet_deltacn_type" label="Comet (deltacn) Normalization" type="select"><expand macro="normalizationOptions" /></param>
160 </section>
161 <section name="comet_expect" title="Comet (expect) Score/Weight" expanded="False">
162 <param name="comet_expect_weight" label="Comet (expect) Weight" type="float" min="-1" max="1" value="-1" />
163 <param name="comet_expect_type" label="Comet (expect) Normalization" type="select"><expand macro="normalizationOptions" /></param>
164 </section>
165 <repeat name="extra_score" title="Extra Search Engine Score/Weight">
166 <param name="extra_score_name" label="Name" type="text" help="For scores in the PSI-MS controlled vocabulary, this field must match the name for that score; for other scores, the UserParam name or pepXML name will suffice." value="SearchEngineName" />
167 <param name="extra_score_normalization" label="Normalization Method" type="select"><expand macro="normalizationOptions" /></param>
168 <param name="extra_score_weight" label="Weight" type="float" help="Negative weights indicate that a lower score is better (e.g. expectation value, p-value)." min="-1" max="1" value="1" />
169 </repeat>
170 </section>
171 </inputs>
172 <outputs>
173 <data format="idpdb" name="output" from_work_dir="output" />
174 </outputs>
175 <tests>
176 <test>
177 <param name="input" value="input/201208-378803-myrimatch.pepXML" />
178 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
179 <param name="MaxFDR" value="0.05" />
180 <output name="output" file="201208-378803-myrimatch.idpDB" compare="sim_size" delta="500000" />
181 </test>
182 <test>
183 <param name="input" value="input/201208-378803-cm.pep.xml" />
184 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
185 <param name="MaxFDR" value="0.05" />
186 <output name="output" file="201208-378803-cm.idpDB" compare="sim_size" delta="500000" />
187 </test>
188 <test>
189 <param name="input" value="input/201208-378803-msgf.mzid" />
190 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
191 <param name="MaxFDR" value="0.05" />
192 <output name="output" file="201208-378803-msgf.idpDB" compare="sim_size" delta="500000" />
193 </test>
194 </tests>
195 <help>
196 <![CDATA[
197 **What it does**
198
199 Creates IDPicker 3 idpDB files from pepXML and mzIdentML files. The input files should be unfiltered and must come from a target/decoy database search.
200 ]]>
201 </help>
202 <citations>
203 <citation type="doi">10.1021/pr900360j</citation>
204 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
205 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
206 </citations>
207 </tool>