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comparison unipept.xml @ 4:4953dcd7dd39 draft

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planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
author galaxyp
date Wed, 23 Jan 2019 09:16:38 -0500
parents 34758ab8aaa4
children 917fd3ebc223
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3:34758ab8aaa4 4:4953dcd7dd39
1 <tool id="unipept" name="Unipept" version="2.0.1"> 1 <tool id="unipept" name="Unipept" version="4.0.0">
2 <description>retrieve taxonomy for peptides</description> 2 <description>retrieve taxonomy for peptides</description>
3 <macros> 3 <macros>
4 <xml name="equate_il"> 4 <xml name="equate_il">
5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine"> 5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help> 6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
20 <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" > 20 <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >
21 <help>return the names in complete taxonomic lineage</help> 21 <help>return the names in complete taxonomic lineage</help>
22 </param> 22 </param>
23 <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" > 23 <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >
24 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help> 24 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
25 </param>
26 </xml>
27 <xml name="domains">
28 <param name="domains" type="boolean" truevalue="-D" falsevalue="" checked="false" label="group responses by GO namespace (biological process, molecular function, cellular component)">
29 <yield/>
30 </param>
31 </xml>
32 <xml name="selected_outputs">
33 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
34 <option value="tsv" selected="true">Tabular with one line per peptide</option>
35 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
36 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
37 <yield/>
38 <option value="unmatched">Unmatched peptides</option>
25 </param> 39 </param>
26 </xml> 40 </xml>
27 </macros> 41 </macros>
28 <requirements> 42 <requirements>
29 <requirement type="package" version="2.7">python</requirement> 43 <requirement type="package" version="2.7">python</requirement>
31 <stdio> 45 <stdio>
32 <exit_code range="1:" /> 46 <exit_code range="1:" />
33 </stdio> 47 </stdio>
34 <command><![CDATA[ 48 <command><![CDATA[
35 python '$__tool_directory__/unipept.py' 49 python '$__tool_directory__/unipept.py'
50 ## --url 'http://morty.ugent.be/api/v1' -g -M 1
36 --api=$unipept.api 51 --api=$unipept.api
37 $unipept.equate_il $unipept.extra 52 $unipept.equate_il $unipept.extra
38 #if $unipept.api != 'pept2prot': 53 #if $unipept.api in ['pept2lca', 'pept2taxa', 'peptinfo']:
39 $unipept.names $unipept.allfields 54 $unipept.names $unipept.allfields
55 #end if
56 #if $unipept.api in ['pept2go', 'pept2funct', 'peptinfo']:
57 $unipept.domains
40 #end if 58 #end if
41 $strict 59 $strict
42 #if str($peptide_src.fmt) == 'proteomic': 60 #if str($peptide_src.fmt) == 'proteomic':
43 #if $peptide_src.input.datatype.file_ext == 'fasta': 61 #if $peptide_src.input.datatype.file_ext == 'fasta':
44 --fasta="$peptide_src.input" 62 --fasta="$peptide_src.input"
56 #elif str($peptide_src.fmt) == 'mzid': 74 #elif str($peptide_src.fmt) == 'mzid':
57 --mzid="$peptide_src.input_mzid" 75 --mzid="$peptide_src.input_mzid"
58 #elif str($peptide_src.fmt) == 'pepxml': 76 #elif str($peptide_src.fmt) == 'pepxml':
59 --pepxml="$peptide_src.input_pepxml" 77 --pepxml="$peptide_src.input_pepxml"
60 #end if 78 #end if
61 #if 'json' in str($outputs).split(',') and str($unipept.api) != 'pept2prot': 79 #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']:
62 --json $output_json 80 --json $output_json
63 #end if 81 #end if
64 #if 'tsv' in str($outputs).split(','): 82 #if 'ec_json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
83 --ec_json $output_ec_json
84 #end if
85 #if 'tsv' in str($selected_outputs).split(','):
65 --tsv $output_tsv 86 --tsv $output_tsv
66 #end if 87 #end if
67 #if 'csv' in str($outputs).split(','): 88 #if 'csv' in str($selected_outputs).split(','):
68 --csv $output_csv 89 --csv $output_csv
69 #end if 90 #end if
70 #if 'unmatched' in str($outputs).split(','): 91 #if 'ec_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
92 --ec_tsv $output_ec_tsv
93 #end if
94 #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
95 --go_tsv $output_go_tsv
96 #end if
97 #if 'unmatched' in str($selected_outputs).split(','):
71 --unmatched $output_unmatched 98 --unmatched $output_unmatched
72 #end if 99 #end if
73 ]]></command> 100 ]]></command>
74 <inputs> 101 <inputs>
75 <conditional name="unipept"> 102 <conditional name="unipept">
76 <param name="api" type="select" label="Unipept application" > 103 <param name="api" type="select" label="Unipept application" >
77 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option> 104 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
78 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option> 105 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
79 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option> 106 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
107 <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
108 <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
109 <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
110 <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
80 </param> 111 </param>
81 <when value="pept2lca"> 112 <when value="pept2lca">
82 <expand macro="equate_il" /> 113 <expand macro="equate_il" />
83 <expand macro="extra"> 114 <expand macro="extra">
84 <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help> 115 <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
97 <expand macro="extra"> 128 <expand macro="extra">
98 <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids 129 <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
99 WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required. 130 WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required.
100 </help> 131 </help>
101 </expand> 132 </expand>
133 </when>
134 <when value="pept2ec">
135 <expand macro="equate_il" />
136 <expand macro="extra_true">
137 <help>Return the name of the EC-number.
138 </help>
139 </expand>
140 </when>
141 <when value="pept2go">
142 <expand macro="equate_il" />
143 <expand macro="extra_true">
144 <help>Return the name of the GO-term.
145 </help>
146 </expand>
147 <expand macro="domains" />
148 </when>
149 <when value="pept2funct">
150 <expand macro="equate_il" />
151 <expand macro="extra_true">
152 <help>Return the name of the EC-number and GO-term.
153 </help>
154 </expand>
155 <expand macro="domains" />
156 </when>
157 <when value="peptinfo">
158 <expand macro="equate_il" />
159 <expand macro="extra_true">
160 <help>Return the name of the EC-number and GO-term.
161 </help>
162 </expand>
163 <expand macro="domains" />
164 <expand macro="names" />
102 </when> 165 </when>
103 </conditional> 166 </conditional>
104 <conditional name="peptide_src"> 167 <conditional name="peptide_src">
105 <param name="fmt" type="select" label="Peptides input format" > 168 <param name="fmt" type="select" label="Peptides input format" >
106 <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option> 169 <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option>
124 </when> 187 </when>
125 <when value="pepxml"> 188 <when value="pepxml">
126 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" /> 189 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
127 </when> 190 </when>
128 </conditional> 191 </conditional>
129 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> 192 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
130 <option value="tsv" selected="true">tabular</option> 193 <option value="tsv" selected="true">Tabular with one line per peptide</option>
131 <option value="csv">Comma Separated Values (.csv)</option> 194 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
132 <option value="json">JSON Taxomony Tree (ignored for pept2prot)</option> 195 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
196 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
197 <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
198 <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
133 <option value="unmatched">Unmatched peptides</option> 199 <option value="unmatched">Unmatched peptides</option>
134 </param> 200 </param>
135 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/> 201 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
136 </inputs> 202 </inputs>
137 <outputs> 203 <outputs>
138 <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} json"> 204 <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json">
139 <filter>'json' in outputs and unipept['api'] != 'pept2prot'</filter> 205 <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
140 <change_format> 206 <change_format>
141 <when input="api" value="pept2prot" format="json" /> 207 <when input="api" value="pept2prot" format="json" />
142 </change_format> 208 </change_format>
143 </data> 209 </data>
210 <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
211 <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
212 </data>
144 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> 213 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
145 <filter>'tsv' in outputs</filter> 214 <filter>'tsv' in selected_outputs</filter>
215 <actions>
216 <action name="comment_lines" type="metadata" default="1" />
217 <!--
218 <conditional name="unipept.api">
219 <when value="pept2funct">
220 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" />
221 </when>
222 <when value="pept2go">
223 <action name="column_names" type="metadata" default="peptide,total_protein_count,go_terms,go_protein_counts,go_names" />
224 </when>
225 <when value="pept2ec">
226 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
227 </when>
228 </conditional>
229 -->
230 </actions>
146 </data> 231 </data>
147 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> 232 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">
148 <filter>'csv' in outputs</filter> 233 <filter>'csv' in selected_outputs</filter>
234 </data>
235 <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv">
236 <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
237 <actions>
238 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" />
239 </actions>
240 </data>
241 <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv">
242 <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
243 <actions>
244 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
245 </actions>
149 </data> 246 </data>
150 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched"> 247 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched">
151 <filter>'unmatched' in outputs</filter> 248 <filter>'unmatched' in selected_outputs</filter>
249 <actions>
250 <action name="column_names" type="metadata" default="Unmatched Peptide" />
251 </actions>
152 </data> 252 </data>
153 </outputs> 253 </outputs>
154 <tests> 254 <tests>
155 <test> 255 <test>
156 <param name="api" value="pept2lca"/> 256 <param name="api" value="pept2lca"/>
157 <param name="fmt" value="tabular"/> 257 <param name="fmt" value="tabular"/>
158 <param name="input_tsv" value="tryptic.tsv"/> 258 <param name="input_tsv" value="tryptic.tsv"/>
159 <param name="column" value="2"/> 259 <param name="column" value="2"/>
160 <param name="extra" value="True"/> 260 <param name="extra" value="True"/>
161 <param name="names" value="True"/> 261 <param name="names" value="True"/>
162 <param name="outputs" value="tsv,unmatched"/> 262 <param name="selected_outputs" value="tsv,unmatched"/>
163 <output name="output_tsv"> 263 <output name="output_tsv">
164 <assert_contents> 264 <assert_contents>
165 <has_text text="Homininae" /> 265 <has_text text="Homininae" />
166 </assert_contents> 266 </assert_contents>
167 </output> 267 </output>
176 <param name="fmt" value="fasta"/> 276 <param name="fmt" value="fasta"/>
177 <param name="input_fasta" value="peptide.fa"/> 277 <param name="input_fasta" value="peptide.fa"/>
178 <param name="equate_il" value="True"/> 278 <param name="equate_il" value="True"/>
179 <param name="extra" value="True"/> 279 <param name="extra" value="True"/>
180 <param name="names" value="True"/> 280 <param name="names" value="True"/>
181 <param name="outputs" value="json,tsv"/> 281 <param name="selected_outputs" value="json,tsv"/>
182 <output name="output_json"> 282 <output name="output_json">
183 <assert_contents> 283 <assert_contents>
184 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" /> 284 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
185 </assert_contents> 285 </assert_contents>
186 </output> 286 </output>
187 <output name="output_tsv"> 287 <output name="output_tsv">
188 <assert_contents> 288 <assert_contents>
189 <has_text text="9606" /> 289 <has_text text="9606" />
190 <has_text text="9598" /> 290 <has_text text="9596" />
191 </assert_contents> 291 </assert_contents>
192 </output> 292 </output>
193 </test> 293 </test>
194 <test> 294 <test>
195 <param name="api" value="pept2taxa"/> 295 <param name="api" value="pept2taxa"/>
196 <param name="fmt" value="fasta"/> 296 <param name="fmt" value="fasta"/>
197 <param name="input_fasta" value="peptide.fa"/> 297 <param name="input_fasta" value="peptide.fa"/>
198 <param name="equate_il" value="True"/> 298 <param name="equate_il" value="True"/>
199 <param name="extra" value="False"/> 299 <param name="extra" value="False"/>
200 <param name="names" value="False"/> 300 <param name="names" value="False"/>
201 <param name="outputs" value="tsv"/> 301 <param name="selected_outputs" value="tsv"/>
202 <output name="output_tsv"> 302 <output name="output_tsv">
203 <assert_contents> 303 <assert_contents>
204 <has_text text="sapiens" /> 304 <has_text text="sapiens" />
205 <has_text text="troglodytes" /> 305 <has_text text="paniscus" />
206 <has_text text="Gorilla" /> 306 <has_text text="Gorilla" />
207 <has_text text="Macaca" /> 307 </assert_contents>
308 </output>
309 </test>
310 <test>
311 <param name="api" value="pept2funct"/>
312 <param name="fmt" value="tabular"/>
313 <param name="input_tsv" value="input.tsv"/>
314 <param name="column" value="2"/>
315 <param name="extra" value="True"/>
316 <param name="names" value="True"/>
317 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,unmatched"/>
318 <output name="output_tsv">
319 <assert_contents>
320 <has_text text="GO:0004802" />
321 <has_text text="2.2.1.1" />
322 </assert_contents>
323 </output>
324 <output name="output_ec_tsv">
325 <assert_contents>
326 <has_text text="2.2.1.1" />
327 </assert_contents>
328 </output>
329 <output name="output_go_tsv">
330 <assert_contents>
331 <has_text text="GO:0004802" />
208 </assert_contents> 332 </assert_contents>
209 </output> 333 </output>
210 </test> 334 </test>
211 </tests> 335 </tests>
212 <help><![CDATA[ 336 <help><![CDATA[
333 species_id 457 species_id
334 subspecies_id 458 subspecies_id
335 varietas_id 459 varietas_id
336 forma_id 460 forma_id
337 461
462 **pept2ec** - http://unipept.ugent.be/apidocs/pept2ec
463
464 Returns the functional EC-numbers associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
465
466 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
467
468 peptide: the peptide that matched this record
469 total_protein_count: Total amount of proteins matched with the given peptide
470 ec_number: EC-number associated with the current tryptic peptide.
471 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
472 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
473
474
475 **pept2go** - http://unipept.ugent.be/apidocs/pept2go
476
477 Returns the functional GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
478
479 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
480
481 peptide: the peptide that matched this record
482 total_protein_count: Total amount of proteins matched with the given peptide
483 go_term: The GO-term associated with the current tryptic peptide.
484 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
485 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
486
487
488 **pept2funct** - http://unipept.ugent.be/apidocs/pept2funct
489
490 Returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
491
492 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
493
494 peptide: the peptide that matched this record
495 total_protein_count: Total amount of proteins matched with the given peptide
496 ec_number: EC-number associated with the current tryptic peptide.
497 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
498 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
499 go_term: The GO-term associated with the current tryptic peptide.
500 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
501 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
502
338 503
339 **Attributions** 504 **Attributions**
340 505
341 The Unipept metaproteomics analysis pipeline 506 The Unipept metaproteomics analysis pipeline
342 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1 507 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1