Mercurial > repos > galaxyp > unipept
annotate unipept.xml @ 2:503ab8a39006 draft
planemo upload for repository http://unipept.ugent.be/apidocs commit b4871f9659a924a68430aed3a93f4f9bad733fd6
| author | galaxyp |
|---|---|
| date | Wed, 07 Dec 2016 16:44:07 -0500 |
| parents | 0c1ee95282fa |
| children | 34758ab8aaa4 |
| rev | line source |
|---|---|
| 1 | 1 <tool id="unipept" name="Unipept" version="1.1.0"> |
| 0 | 2 <description>retrieve taxonomy for peptides</description> |
| 3 <macros> | |
| 4 <xml name="equate_il"> | |
| 1 | 5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine"> |
| 0 | 6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help> |
| 7 </param > | |
| 8 </xml> | |
| 9 <xml name="extra"> | |
| 10 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information"> | |
| 11 <yield/> | |
| 12 </param > | |
| 13 </xml> | |
| 14 <xml name="names"> | |
| 15 <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" > | |
| 1 | 16 <help>return the names in complete taxonomic lineage</help> |
| 17 </param > | |
| 18 <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" > | |
| 19 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help> | |
| 0 | 20 </param > |
| 21 </xml> | |
| 22 </macros> | |
| 23 <requirements> | |
|
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503ab8a39006
planemo upload for repository http://unipept.ugent.be/apidocs commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
1
diff
changeset
|
24 <requirement type="package" version="2.7.12">python</requirement> |
| 0 | 25 </requirements> |
| 26 <stdio> | |
| 27 <exit_code range="1:" /> | |
| 28 </stdio> | |
| 29 <command interpreter="python"><![CDATA[ | |
| 30 unipept.py | |
| 31 --api=$unipept.api | |
| 32 $unipept.equate_il $unipept.extra | |
| 33 #if $unipept.api != 'pept2prot': | |
| 1 | 34 $unipept.names $unipept.allfields |
| 0 | 35 #end if |
| 36 $strict | |
| 37 #if str($peptide_src.fmt) == 'proteomic': | |
| 38 #if $peptide_src.input.datatype.file_ext == 'fasta': | |
| 39 --fasta="$peptide_src.input" | |
| 40 #elif $peptide_src.input.datatype.file_ext == 'mzid': | |
| 41 --mzid="$peptide_src.input" | |
| 42 #elif $peptide_src.input.datatype.file_ext == 'pepxml': | |
| 43 --pepxml="$peptide_src.input" | |
| 44 #end if | |
| 45 #elif str($peptide_src.fmt) == 'tabular': | |
| 46 --tabular="$peptide_src.input_tsv" | |
| 47 #set $col = int(str($peptide_src.column)) - 1 | |
| 48 --column=$col | |
| 49 #elif str($peptide_src.fmt) == 'fasta': | |
| 50 --fasta="$peptide_src.input_fasta" | |
| 51 #elif str($peptide_src.fmt) == 'mzid': | |
| 52 --mzid="$peptide_src.input_mzid" | |
| 53 #elif str($peptide_src.fmt) == 'pepxml': | |
| 54 --pepxml="$peptide_src.input_pepxml" | |
| 55 #end if | |
| 56 #if 'json' in str($outputs).split(','): | |
| 57 --json $output_json | |
| 58 #end if | |
| 59 #if 'tsv' in str($outputs).split(','): | |
| 60 --tsv $output_tsv | |
| 61 #end if | |
| 62 #if 'csv' in str($outputs).split(','): | |
| 63 --csv $output_csv | |
| 64 #end if | |
| 1 | 65 #if 'unmatched' in str($outputs).split(','): |
| 66 --unmatched $output_unmatched | |
| 0 | 67 #end if |
| 68 ]]></command> | |
| 69 <inputs> | |
| 70 <conditional name="unipept"> | |
| 71 <param name="api" type="select" label="Unipept application" > | |
| 1 | 72 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option> |
| 73 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option> | |
| 0 | 74 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option> |
| 75 </param> | |
| 1 | 76 <when value="pept2lca"> |
| 77 <expand macro="equate_il" /> | |
| 78 <expand macro="extra"> | |
| 79 <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help> | |
| 80 </expand> | |
| 81 <expand macro="names" /> | |
| 82 </when> | |
| 0 | 83 <when value="pept2taxa"> |
| 84 <expand macro="equate_il" /> | |
| 85 <expand macro="extra"> | |
| 86 <checked>true</checked> | |
| 1 | 87 <help>Return the complete lineage of each organism, and include ID fields.</help> |
| 0 | 88 </expand> |
| 89 <expand macro="names" /> | |
| 90 </when> | |
| 91 <when value="pept2prot"> | |
| 92 <expand macro="equate_il" /> | |
| 93 <expand macro="extra"> | |
| 94 <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids | |
| 95 WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required. | |
| 96 </help> | |
| 97 </expand> | |
| 98 </when> | |
| 99 </conditional> | |
| 100 <conditional name="peptide_src"> | |
| 101 <param name="fmt" type="select" label="Peptides input format" > | |
| 102 <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option> | |
| 103 <option value="tabular">tabular</option> | |
| 104 <option value="fasta">fasta</option> | |
| 105 <option value="mzid">mzid</option> | |
| 106 <option value="pepxml">pepxml</option> | |
| 107 </param> | |
| 108 <when value="proteomic"> | |
| 109 <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" /> | |
| 110 </when> | |
| 111 <when value="tabular"> | |
| 112 <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" /> | |
| 113 <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" /> | |
| 114 </when> | |
| 115 <when value="fasta"> | |
| 116 <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" /> | |
| 117 </when> | |
| 118 <when value="mzid"> | |
| 119 <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" /> | |
| 120 </when> | |
| 121 <when value="pepxml"> | |
| 122 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" /> | |
| 123 </when> | |
| 124 </conditional> | |
| 125 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> | |
| 126 <option value="tsv" selected="true">tabular</option> | |
| 127 <option value="csv">Comma Separated Values (.csv)</option> | |
| 128 <option value="json">JSON</option> | |
| 1 | 129 <option value="unmatched">Unmatched peptides</option> |
| 0 | 130 </param> |
| 131 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/> | |
| 132 </inputs> | |
| 133 <outputs> | |
| 134 <data name="output_json" format="json" label="${tool.name} ${unipept.api} on ${on_string} json"> | |
| 135 <filter>'json' in outputs</filter> | |
| 136 </data> | |
| 137 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> | |
| 138 <filter>'tsv' in outputs</filter> | |
| 139 </data> | |
| 140 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> | |
| 141 <filter>'csv' in outputs</filter> | |
| 142 </data> | |
| 1 | 143 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched"> |
| 144 <filter>'unmatched' in outputs</filter> | |
| 0 | 145 </data> |
| 146 </outputs> | |
| 147 <tests> | |
| 148 <test> | |
| 1 | 149 <param name="api" value="pept2lca"/> |
| 0 | 150 <param name="fmt" value="tabular"/> |
| 1 | 151 <param name="input_tsv" value="tryptic.tsv"/> |
| 0 | 152 <param name="column" value="2"/> |
| 153 <param name="extra" value="True"/> | |
| 154 <param name="names" value="True"/> | |
| 1 | 155 <param name="outputs" value="tsv,unmatched"/> |
| 0 | 156 <output name="output_tsv"> |
| 157 <assert_contents> | |
| 1 | 158 <has_text text="Homininae" /> |
| 0 | 159 </assert_contents> |
| 160 </output> | |
| 1 | 161 <output name="output_unmatched"> |
| 0 | 162 <assert_contents> |
| 1 | 163 <has_text text="QTAMAV" /> |
| 0 | 164 </assert_contents> |
| 165 </output> | |
| 166 </test> | |
| 167 <test> | |
| 1 | 168 <param name="api" value="pept2lca"/> |
| 0 | 169 <param name="fmt" value="fasta"/> |
| 1 | 170 <param name="input_fasta" value="peptide.fa"/> |
| 0 | 171 <param name="equate_il" value="True"/> |
| 172 <param name="extra" value="True"/> | |
| 173 <param name="names" value="True"/> | |
| 1 | 174 <param name="outputs" value="json,tsv"/> |
| 0 | 175 <output name="output_json"> |
| 176 <assert_contents> | |
| 1 | 177 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" /> |
| 178 </assert_contents> | |
| 179 </output> | |
| 180 <output name="output_tsv"> | |
| 181 <assert_contents> | |
| 182 <has_text text="9606" /> | |
| 183 <has_text text="9598" /> | |
| 0 | 184 </assert_contents> |
| 185 </output> | |
| 1 | 186 </test> |
| 187 <test> | |
| 188 <param name="api" value="pept2taxa"/> | |
| 189 <param name="fmt" value="fasta"/> | |
| 190 <param name="input_fasta" value="peptide.fa"/> | |
| 191 <param name="equate_il" value="True"/> | |
| 192 <param name="extra" value="False"/> | |
| 193 <param name="names" value="False"/> | |
| 194 <param name="outputs" value="tsv"/> | |
| 195 <output name="output_tsv"> | |
| 0 | 196 <assert_contents> |
| 1 | 197 <has_text text="sapiens" /> |
| 198 <has_text text="troglodytes" /> | |
| 199 <has_text text="Gorilla" /> | |
| 200 <has_text text="Macaca" /> | |
| 0 | 201 </assert_contents> |
| 202 </output> | |
| 203 </test> | |
| 204 </tests> | |
| 205 <help><![CDATA[ | |
| 206 **Unipept** | |
| 207 | |
| 208 Retrieve Uniprot and taxanomic information for trypic peptides. | |
| 1 | 209 |
| 210 Unipept API documentation - http://unipept.ugent.be/apidocs | |
| 0 | 211 |
| 1 | 212 **Input** |
| 213 | |
| 214 Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets. | |
| 215 | |
| 216 Processing deatils:: | |
| 217 | |
| 218 The input peptides are split into typtic peptide fragments in order to match the Unipept records. | |
| 219 Only fragments that are complete tryptic peptides between 5 and 50 animo acid in length will be matched by Unipept. | |
| 220 The match to the most specific tryptic fragment is reported. | |
| 221 | |
| 222 | |
| 223 **Unipept APIs** | |
| 224 | |
| 225 **pept2prot** - http://unipept.ugent.be/apidocs/pept2prot | |
| 226 | |
| 0 | 227 Returns the list of UniProt entries containing a given tryptic peptide. This is the same information as provided on the Protein matches tab when performing a search with the Tryptic Peptide Analysis in the web interface. |
| 228 | |
| 229 By default, each object contains the following information fields extracted from the UniProt record:: | |
| 230 | |
| 231 peptide: the peptide that matched this record | |
| 232 uniprot_id: the UniProt accession number of the matching record | |
| 233 taxon_id: the NCBI taxon id of the organism associated with the matching record | |
| 234 | |
| 235 When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt record:: | |
| 236 | |
| 237 taxon_name: the name of the organism associated with the matching UniProt record | |
| 238 ec_references: a space separated list of associated EC numbers | |
| 239 go_references: a space separated list of associated GO terms | |
| 240 refseq_ids: a space separated list of associated RefSeq accession numbers | |
| 241 refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers | |
| 242 insdc_ids: a space separated list of associated insdc accession numbers | |
| 243 insdc_protein_ids: a space separated list of associated insdc protein accession numbers | |
| 244 | |
| 245 | |
| 1 | 246 **pept2taxa** - http://unipept.ugent.be/apidocs/pept2taxa |
| 247 | |
| 0 | 248 Returns the set of organisms associated with the UniProt entries containing a given tryptic peptide. This is the same information as provided on the Lineage table tab when performing a search with the Tryptic Peptide Analysis in the web interface. |
| 249 | |
| 250 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: | |
| 251 | |
| 252 peptide: the peptide that matched this record | |
| 253 taxon_id: the NCBI taxon id of the organism associated with the matching record | |
| 254 taxon_name: the name of the organism associated with the matching record | |
| 255 taxon_rank: the taxonomic rank of the organism associated with the matching record | |
| 256 | |
| 257 When the extra parameter is set to true, objects contain additional information about the lineages of the organism extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields:: | |
| 258 | |
| 259 superkingdom_id | |
| 260 kingdom_id | |
| 261 subkingdom_id | |
| 262 superphylum_id | |
| 263 phylum_id | |
| 264 subphylum_id | |
| 265 superclass_id | |
| 266 class_id | |
| 267 subclass_id | |
| 268 infraclass_id | |
| 269 superorder_id | |
| 270 order_id | |
| 271 suborder_id | |
| 272 infraorder_id | |
| 273 parvorder_id | |
| 274 superfamily_id | |
| 275 family_id | |
| 276 subfamily_id | |
| 277 tribe_id | |
| 278 subtribe_id | |
| 279 genus_id | |
| 280 subgenus_id | |
| 281 species_group_id | |
| 282 species_subgroup_id | |
| 283 species_id | |
| 284 subspecies_id | |
| 285 varietas_id | |
| 286 forma_id | |
| 287 | |
| 288 | |
| 1 | 289 **pept2lca** - http://unipept.ugent.be/apidocs/pept2lca |
| 290 | |
| 0 | 291 Returns the taxonomic lowest common ancestor for a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface. |
| 292 | |
| 293 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: | |
| 294 | |
| 295 peptide: the peptide that matched this record | |
| 296 taxon_id: the NCBI taxon id of the organism associated with the matching record | |
| 297 taxon_name: the name of the organism associated with the matching record | |
| 298 taxon_rank: the taxonomic rank of the organism associated with the matching record | |
| 299 | |
| 300 When the extra parameter is set to true, objects contain additional information about the lineage of the taxonomic lowest common ancestor extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields:: | |
| 301 | |
| 302 superkingdom_id | |
| 303 kingdom_id | |
| 304 subkingdom_id | |
| 305 superphylum_id | |
| 306 phylum_id | |
| 307 subphylum_id | |
| 308 superclass_id | |
| 309 class_id | |
| 310 subclass_id | |
| 311 infraclass_id | |
| 312 superorder_id | |
| 313 order_id | |
| 314 suborder_id | |
| 315 infraorder_id | |
| 316 parvorder_id | |
| 317 superfamily_id | |
| 318 family_id | |
| 319 subfamily_id | |
| 320 tribe_id | |
| 321 subtribe_id | |
| 322 genus_id | |
| 323 subgenus_id | |
| 324 species_group_id | |
| 325 species_subgroup_id | |
| 326 species_id | |
| 327 subspecies_id | |
| 328 varietas_id | |
| 329 forma_id | |
| 330 | |
| 331 | |
| 332 **Attributions** | |
| 333 | |
| 334 The Unipept metaproteomics analysis pipeline | |
| 335 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1 | |
| 336 Article first published online: 11 FEB 2015 | |
| 337 DOI: 10.1002/pmic.201400361 | |
| 338 http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400361/abstract;jsessionid=BFF1994E4C14DA73D7C907EB208AD710.f04t04 | |
| 339 | |
| 340 ]]></help> | |
| 341 <citations> | |
| 342 <citation type="doi">doi:10.1002/pmic.201400361</citation> | |
| 343 </citations> | |
| 344 | |
| 345 </tool> |