Mercurial > repos > galaxyp > proteomiqon_proteininference

comparison proteomiqon_proteininference.xml @ 1:7729b9043b80 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference commit 6c26a48bade20a6be46dec57602579ffc05cbe27"
author galaxyp
date Fri, 29 Apr 2022 19:29:14 +0000
parents 8e4fb95a319a
children
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equal deleted inserted replaced
0:8e4fb95a319a 1:7729b9043b80
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #import re 12 #import re
13 #if $PSMInputModeCond.PSMInputMode == "single" 13 #if $PSMInputModeCond.PSMInputMode == "single"
14 #set basename = $re.sub(r'[^\w ,.\-+]','_',$PSMInputModeCond.scoredPSMs.element_identifier) 14 #set basename = $re.sub(r'[^\w ,.\-+]','_',$PSMInputModeCond.scoredPSMs.element_identifier)
15 ln -s '$scoredPSMs' '${basename}.qpsm' && 15 ln -s '$scoredPSMs' '${basename}.qpsm' &&
16 mkdir './out' &&
17 ln -s '$out_prot' './out/${basename}.prot' &&
16 #elif $PSMInputModeCond.PSMInputMode == "multi" 18 #elif $PSMInputModeCond.PSMInputMode == "multi"
17 #for $psmfile in $PSMInputModeCond.scoredPSMs 19 #for $psmfile in $PSMInputModeCond.scoredPSMs
18 #set basename = $re.sub(r'[^\w ,.\-+]','_',$psmfile.element_identifier) 20 #set basename = $re.sub(r'[^\w ,.\-+]','_',$psmfile.element_identifier)
19 ln -s '$psmfile' '${basename}.qpsm' && 21 ln -s '$psmfile' '${basename}.qpsm' &&
20 #end for 22 #end for
34 "Case": "${Protein}" 36 "Case": "${Protein}"
35 }, 37 },
36 "Peptide": { 38 "Peptide": {
37 "Case": "${Peptide}" 39 "Case": "${Peptide}"
38 }, 40 },
39 "GroupFiles": ${GroupFiles}, 41 #if $PSMInputModeCond.PSMInputMode == "multi"
42 "GroupFiles": ${PSMInputModeCond.GroupFiles},
43 #else
44 "GroupFiles": false,
45 #end if
40 #if $GetQValueCond.GetQValue == "LogisticRegression" 46 #if $GetQValueCond.GetQValue == "LogisticRegression"
41 "GetQValue": { 47 "GetQValue": {
42 "Case": "${GetQValueCond.GetQValue}", 48 "Case": "${GetQValueCond.GetQValue}",
43 "Fields": [ 49 "Fields": [
44 { 50 {
65 <when value="single"> 71 <when value="single">
66 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM file" help="Specify peptide identifications." /> 72 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM file" help="Specify peptide identifications." />
67 </when> 73 </when>
68 <when value="multi"> 74 <when value="multi">
69 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM files" help="Specify list of peptide identifications." multiple="true"/> 75 <param name="scoredPSMs" type="data" format="tabular" label="Scored PSM files" help="Specify list of peptide identifications." multiple="true"/>
76 <param name="GroupFiles" type="boolean" checked="true" label="Groupe files" help="If checked, protein inference is carried out using peptide information from all files simultaneously."/>
70 </when> 77 </when>
71 </conditional> 78 </conditional>
72 <param name="ProteinIdentifierRegex" type="text" value="id" label="Protein identifier regex pattern" help="Fasta headers do often contain additional information in addition to your protein identifier, by specifying a regex pattern the tool can extract the protein IDs. If you fasta headers are already cleaned you can leave this field empty."> 79 <param name="ProteinIdentifierRegex" type="text" value="id" label="Protein identifier regex pattern" help="Fasta headers do often contain additional information in addition to your protein identifier, by specifying a regex pattern the tool can extract the protein IDs. If you fasta headers are already cleaned you can leave this field empty.">
73 <sanitizer sanitize="false" /> 80 <sanitizer sanitize="false" />
74 </param> 81 </param>
79 <param name="Peptide" type="select" label="Peptide" help="Specify how peptides are used to infer protein groups. For details please refer to the description below."> 86 <param name="Peptide" type="select" label="Peptide" help="Specify how peptides are used to infer protein groups. For details please refer to the description below.">
80 <option value="Minimal" selected="true">Minimal</option> 87 <option value="Minimal" selected="true">Minimal</option>
81 <option value="Maximal">Maximal</option> 88 <option value="Maximal">Maximal</option>
82 <option value="MaximalInverse">MaximalInverse</option> 89 <option value="MaximalInverse">MaximalInverse</option>
83 </param> 90 </param>
84 <param name="GroupFiles" type="boolean" checked="true" label="Groupe files" help="If checked, protein inference is carried out using peptide information from all files simultaneously."/>
85 <conditional name="GetQValueCond"> 91 <conditional name="GetQValueCond">
86 <param name="GetQValue" type="select" label="Q-Value method" help="Specify if and how q-value calculation should be carried out."> 92 <param name="GetQValue" type="select" label="Q-Value method" help="Specify if and how q-value calculation should be carried out.">
87 <option value="Storey" selected="true">Storey</option> 93 <option value="Storey" selected="true">Storey</option>
88 <option value="LogisticRegression">Logistic Regression</option> 94 <option value="LogisticRegression">Logistic Regression</option>
89 <option value="NoQValue">NoQValue</option> 95 <option value="NoQValue">NoQValue</option>
100 </conditional> 106 </conditional>
101 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/> 107 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/>
102 </inputs> 108 </inputs>
103 <outputs> 109 <outputs>
104 <data format="tabular" name="out_prot" > 110 <data format="tabular" name="out_prot" >
105 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.prot" ext="tabular" directory="out" visible="true" assign_primary_output="true" /> 111 <filter>PSMInputModeCond['PSMInputMode'] == 'single'</filter>
106 </data> 112 </data>
113 <collection type="list" format="tabular" name="out_prot_collection" >
114 <discover_datasets pattern="(?P&lt;designation&gt;.+\.prot)" directory="out" />
115 <filter>PSMInputModeCond['PSMInputMode'] == 'multi'</filter>
116 </collection>
107 <data format="json" name="out_paramfile"> 117 <data format="json" name="out_paramfile">
108 <filter>outputParamfile</filter> 118 <filter>outputParamfile</filter>
109 </data> 119 </data>
110 </outputs> 120 </outputs>
111 <tests> 121 <tests>
116 <param name="scoredPSMs" value="sample_1.qpsm"/> 126 <param name="scoredPSMs" value="sample_1.qpsm"/>
117 </conditional> 127 </conditional>
118 <param name="ProteinIdentifierRegex" value="id"/> 128 <param name="ProteinIdentifierRegex" value="id"/>
119 <param name="Protein" value="Minimal"/> 129 <param name="Protein" value="Minimal"/>
120 <param name="Peptide" value="Minimal"/> 130 <param name="Peptide" value="Minimal"/>
121 <param name="GroupFiles" value="true"/>
122 <param name="outputParamfile" value="false"/> 131 <param name="outputParamfile" value="false"/>
123 </test> 132 </test>
124 <test expect_num_outputs="2"> 133 <test expect_num_outputs="2">
125 <param name="peptideDB" value="sample.db"/> 134 <param name="peptideDB" value="sample.db"/>
126 <conditional name="PSMInputModeCond"> 135 <conditional name="PSMInputModeCond">
127 <param name="PSMInputMode" value="single"/> 136 <param name="PSMInputMode" value="single"/>
128 <param name="scoredPSMs" value="sample_1.qpsm"/> 137 <param name="scoredPSMs" value="sample_1.qpsm"/>
138 </conditional>
139 <param name="ProteinIdentifierRegex" value="id"/>
140 <param name="Protein" value="Maximal"/>
141 <param name="Peptide" value="Maximal"/>
142 <conditional name="GetQValueCond">
143 <param name="GetQValue" value="Storey"/>
144 </conditional>
145 <param name="outputParamfile" value="true"/>
146 <output name="out_paramfile" file="result_1.json" />
147 </test>
148 <test expect_num_outputs="2">
149 <param name="peptideDB" value="sample.db"/>
150 <conditional name="PSMInputModeCond">
151 <param name="PSMInputMode" value="single"/>
152 <param name="scoredPSMs" value="sample_1.qpsm"/>
153 </conditional>
154 <param name="ProteinIdentifierRegex" value="id"/>
155 <param name="Protein" value="Minimal"/>
156 <param name="Peptide" value="MaximalInverse"/>
157 <conditional name="GetQValueCond">
158 <param name="GetQValue" value="NoQValue"/>
159 </conditional>
160 <param name="outputParamfile" value="true"/>
161 <output name="out_paramfile" file="result_2.json" />
162 </test>
163 <test expect_num_outputs="2">
164 <param name="peptideDB" value="sample.db"/>
165 <conditional name="PSMInputModeCond">
166 <param name="PSMInputMode" value="single"/>
167 <param name="scoredPSMs" value="sample_1.qpsm"/>
168 </conditional>
169 <param name="ProteinIdentifierRegex" value="id"/>
170 <param name="Protein" value="Minimal"/>
171 <param name="Peptide" value="MaximalInverse"/>
172 <conditional name="GetQValueCond">
173 <param name="GetQValue" value="LogisticRegression"/>
174 <param name="LogisticRegressionType" value="Conservative"/>
175 </conditional>
176 <param name="outputParamfile" value="true"/>
177 <output name="out_paramfile" file="result_3.json" />
178 </test>
179 <test expect_num_outputs="2">
180 <param name="peptideDB" value="sample.db"/>
181 <conditional name="PSMInputModeCond">
182 <param name="PSMInputMode" value="single"/>
183 <param name="scoredPSMs" value="sample_1.qpsm"/>
184 </conditional>
185 <param name="ProteinIdentifierRegex" value="id"/>
186 <param name="Protein" value="Minimal"/>
187 <param name="Peptide" value="MaximalInverse"/>
188 <conditional name="GetQValueCond">
189 <param name="GetQValue" value="LogisticRegression"/>
190 <param name="LogisticRegressionType" value="MAYU"/>
191 </conditional>
192 <param name="outputParamfile" value="true"/>
193 <output name="out_paramfile" file="result_4.json" />
194 </test>
195 <test expect_num_outputs="2">
196 <param name="peptideDB" value="sample.db"/>
197 <conditional name="PSMInputModeCond">
198 <param name="PSMInputMode" value="single"/>
199 <param name="scoredPSMs" value="sample_1.qpsm"/>
200 </conditional>
201 <param name="ProteinIdentifierRegex" value="id"/>
202 <param name="Protein" value="Minimal"/>
203 <param name="Peptide" value="MaximalInverse"/>
204 <conditional name="GetQValueCond">
205 <param name="GetQValue" value="LogisticRegression"/>
206 <param name="LogisticRegressionType" value="DecoyTargetRatio"/>
207 </conditional>
208 <param name="outputParamfile" value="true"/>
209 <output name="out_paramfile" file="result_5.json" />
210 </test>
211 <test expect_num_outputs="2">
212 <param name="peptideDB" value="sample.db"/>
213 <conditional name="PSMInputModeCond">
214 <param name="PSMInputMode" value="multi"/>
215 <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm,sample_3.qpsm"/>
129 </conditional> 216 </conditional>
130 <param name="ProteinIdentifierRegex" value="id"/> 217 <param name="ProteinIdentifierRegex" value="id"/>
131 <param name="Protein" value="Maximal"/> 218 <param name="Protein" value="Maximal"/>
132 <param name="Peptide" value="Maximal"/> 219 <param name="Peptide" value="Maximal"/>
133 <param name="GroupFiles" value="true"/> 220 <param name="GroupFiles" value="true"/>
134 <conditional name="GetQValueCond"> 221 <conditional name="GetQValueCond">
135 <param name="GetQValue" value="Storey"/>
136 </conditional>
137 <param name="outputParamfile" value="true"/>
138 <output name="out_paramfile" file="result_1.json" />
139 </test>
140 <test expect_num_outputs="2">
141 <param name="peptideDB" value="sample.db"/>
142 <conditional name="PSMInputModeCond">
143 <param name="PSMInputMode" value="single"/>
144 <param name="scoredPSMs" value="sample_1.qpsm"/>
145 </conditional>
146 <param name="ProteinIdentifierRegex" value="id"/>
147 <param name="Protein" value="Minimal"/>
148 <param name="Peptide" value="MaximalInverse"/>
149 <param name="GroupFiles" value="true"/>
150 <conditional name="GetQValueCond">
151 <param name="GetQValue" value="NoQValue"/> 222 <param name="GetQValue" value="NoQValue"/>
152 </conditional> 223 </conditional>
153 <param name="outputParamfile" value="true"/> 224 <param name="outputParamfile" value="true"/>
154 <output name="out_paramfile" file="result_2.json" /> 225 <output_collection name="out_prot_collection" type="list" count="3" />
155 </test> 226 <output name="out_paramfile" file="result_6.json" />
156 <test expect_num_outputs="2">
157 <param name="peptideDB" value="sample.db"/>
158 <conditional name="PSMInputModeCond">
159 <param name="PSMInputMode" value="single"/>
160 <param name="scoredPSMs" value="sample_1.qpsm"/>
161 </conditional>
162 <param name="ProteinIdentifierRegex" value="id"/>
163 <param name="Protein" value="Minimal"/>
164 <param name="Peptide" value="MaximalInverse"/>
165 <param name="GroupFiles" value="true"/>
166 <conditional name="GetQValueCond">
167 <param name="GetQValue" value="LogisticRegression"/>
168 <param name="LogisticRegressionType" value="Conservative"/>
169 </conditional>
170 <param name="outputParamfile" value="true"/>
171 <output name="out_paramfile" file="result_3.json" />
172 </test>
173 <test expect_num_outputs="2">
174 <param name="peptideDB" value="sample.db"/>
175 <conditional name="PSMInputModeCond">
176 <param name="PSMInputMode" value="single"/>
177 <param name="scoredPSMs" value="sample_1.qpsm"/>
178 </conditional>
179 <param name="ProteinIdentifierRegex" value="id"/>
180 <param name="Protein" value="Minimal"/>
181 <param name="Peptide" value="MaximalInverse"/>
182 <param name="GroupFiles" value="true"/>
183 <conditional name="GetQValueCond">
184 <param name="GetQValue" value="LogisticRegression"/>
185 <param name="LogisticRegressionType" value="MAYU"/>
186 </conditional>
187 <param name="outputParamfile" value="true"/>
188 <output name="out_paramfile" file="result_4.json" />
189 </test>
190 <test expect_num_outputs="2">
191 <param name="peptideDB" value="sample.db"/>
192 <conditional name="PSMInputModeCond">
193 <param name="PSMInputMode" value="single"/>
194 <param name="scoredPSMs" value="sample_1.qpsm"/>
195 </conditional>
196 <param name="ProteinIdentifierRegex" value="id"/>
197 <param name="Protein" value="Minimal"/>
198 <param name="Peptide" value="MaximalInverse"/>
199 <param name="GroupFiles" value="true"/>
200 <conditional name="GetQValueCond">
201 <param name="GetQValue" value="LogisticRegression"/>
202 <param name="LogisticRegressionType" value="DecoyTargetRatio"/>
203 </conditional>
204 <param name="outputParamfile" value="true"/>
205 <output name="out_paramfile" file="result_5.json" />
206 </test> 227 </test>
207 <test expect_num_outputs="2"> 228 <test expect_num_outputs="2">
208 <param name="peptideDB" value="sample.db"/> 229 <param name="peptideDB" value="sample.db"/>
209 <conditional name="PSMInputModeCond"> 230 <conditional name="PSMInputModeCond">
210 <param name="PSMInputMode" value="multi"/> 231 <param name="PSMInputMode" value="multi"/>
211 <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm,sample_3.qpsm"/> 232 <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm"/>
212 </conditional>
213 <param name="ProteinIdentifierRegex" value="id"/>
214 <param name="Protein" value="Maximal"/>
215 <param name="Peptide" value="Maximal"/>
216 <param name="GroupFiles" value="true"/>
217 <conditional name="GetQValueCond">
218 <param name="GetQValue" value="NoQValue"/>
219 </conditional>
220 <param name="outputParamfile" value="true"/>
221 <output name="out_paramfile" file="result_6.json" />
222 </test>
223 <test expect_num_outputs="2">
224 <param name="peptideDB" value="sample.db"/>
225 <conditional name="PSMInputModeCond">
226 <param name="PSMInputMode" value="multi"/>
227 <param name="scoredPSMs" value="sample_1.qpsm,sample_2.qpsm,sample_3.qpsm"/>
228 </conditional> 233 </conditional>
229 <param name="ProteinIdentifierRegex" value="id"/> 234 <param name="ProteinIdentifierRegex" value="id"/>
230 <param name="Protein" value="Maximal"/> 235 <param name="Protein" value="Maximal"/>
231 <param name="Peptide" value="Maximal"/> 236 <param name="Peptide" value="Maximal"/>
232 <param name="GroupFiles" value="false"/> 237 <param name="GroupFiles" value="false"/>
233 <conditional name="GetQValueCond"> 238 <conditional name="GetQValueCond">
234 <param name="GetQValue" value="NoQValue"/> 239 <param name="GetQValue" value="NoQValue"/>
235 </conditional> 240 </conditional>
236 <param name="outputParamfile" value="true"/> 241 <param name="outputParamfile" value="true"/>
242 <output_collection name="out_prot_collection" type="list" count="2" />
237 <output name="out_paramfile" file="result_7.json" /> 243 <output name="out_paramfile" file="result_7.json" />
238 </test> 244 </test>
239 </tests> 245 </tests>
240 <help> 246 <help>
241 <![CDATA[ 247 <![CDATA[