Mercurial > repos > galaxyp > unipept
diff unipept.xml @ 0:6430407e5869 draft
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| author | galaxyp |
|---|---|
| date | Fri, 03 Apr 2015 14:55:49 -0400 |
| parents | |
| children | 0c1ee95282fa |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/unipept.xml Fri Apr 03 14:55:49 2015 -0400 @@ -0,0 +1,306 @@ +<tool id="unipept" name="Unipept" version="0.1.0"> + <description>retrieve taxonomy for peptides</description> + <macros> + <xml name="equate_il"> + <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Equate isoleucine and leucine"> + <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help> + </param > + </xml> + <xml name="extra"> + <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information"> + <yield/> + </param > + </xml> + <xml name="names"> + <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" > + <help>return the names of taxons</help> + </param > + </xml> + </macros> + <requirements> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command interpreter="python"><![CDATA[ + unipept.py + --api=$unipept.api + $unipept.equate_il $unipept.extra + #if $unipept.api != 'pept2prot': + $unipept.names + #end if + $strict + #if str($peptide_src.fmt) == 'proteomic': + #if $peptide_src.input.datatype.file_ext == 'fasta': + --fasta="$peptide_src.input" + #elif $peptide_src.input.datatype.file_ext == 'mzid': + --mzid="$peptide_src.input" + #elif $peptide_src.input.datatype.file_ext == 'pepxml': + --pepxml="$peptide_src.input" + #end if + #elif str($peptide_src.fmt) == 'tabular': + --tabular="$peptide_src.input_tsv" + #set $col = int(str($peptide_src.column)) - 1 + --column=$col + #elif str($peptide_src.fmt) == 'fasta': + --fasta="$peptide_src.input_fasta" + #elif str($peptide_src.fmt) == 'mzid': + --mzid="$peptide_src.input_mzid" + #elif str($peptide_src.fmt) == 'pepxml': + --pepxml="$peptide_src.input_pepxml" + #end if + #if 'json' in str($outputs).split(','): + --json $output_json + #end if + #if 'tsv' in str($outputs).split(','): + --tsv $output_tsv + #end if + #if 'csv' in str($outputs).split(','): + --csv $output_csv + #end if + #if 'mismatch' in str($outputs).split(','): + --mismatch $output_mismatch + #end if + ]]></command> + <inputs> + <conditional name="unipept"> + <param name="api" type="select" label="Unipept application" > + <option value="pept2taxa" selected="true">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option> + <option value="pept2lca">pept2lca: lowest common ancestor</option> + <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option> + </param> + <when value="pept2taxa"> + <expand macro="equate_il" /> + <expand macro="extra"> + <checked>true</checked> + <help>Return the complete lineage of each organism.</help> + </expand> + <expand macro="names" /> + </when> + <when value="pept2lca"> + <expand macro="equate_il" /> + <expand macro="extra"> + <help>Return the complete lineage of the taxonomic lowest common ancestor.</help> + </expand> + <expand macro="names" /> + </when> + <when value="pept2prot"> + <expand macro="equate_il" /> + <expand macro="extra"> + <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids + WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required. + </help> + </expand> + </when> + </conditional> + <conditional name="peptide_src"> + <param name="fmt" type="select" label="Peptides input format" > + <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option> + <option value="tabular">tabular</option> + <option value="fasta">fasta</option> + <option value="mzid">mzid</option> + <option value="pepxml">pepxml</option> + </param> + <when value="proteomic"> + <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" /> + </when> + <when value="tabular"> + <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" /> + <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" /> + </when> + <when value="fasta"> + <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" /> + </when> + <when value="mzid"> + <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" /> + </when> + <when value="pepxml"> + <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" /> + </when> + </conditional> + <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> + <option value="tsv" selected="true">tabular</option> + <option value="csv">Comma Separated Values (.csv)</option> + <option value="json">JSON</option> + <option value="mismatch">Mismatches</option> + </param> + <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/> + </inputs> + <outputs> + <data name="output_json" format="json" label="${tool.name} ${unipept.api} on ${on_string} json"> + <filter>'json' in outputs</filter> + </data> + <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> + <filter>'tsv' in outputs</filter> + </data> + <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> + <filter>'csv' in outputs</filter> + </data> + <data name="output_mismatch" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} mismatch"> + <filter>'mismatch' in outputs</filter> + </data> + </outputs> + <tests> + <test> + <param name="fmt" value="tabular"/> + <param name="input_tsv" value="input.tsv"/> + <param name="column" value="2"/> + <param name="extra" value="True"/> + <param name="names" value="True"/> + <param name="outputs" value="tsv,mismatch"/> + <output name="output_tsv"> + <assert_contents> + <has_text text="AIPQLEVARPADAYETAEAYR" /> + </assert_contents> + </output> + <output name="output_mismatch"> + <assert_contents> + <has_text text="DQIAHEGK" /> + </assert_contents> + </output> + </test> + <test> + <param name="fmt" value="fasta"/> + <param name="input_tsv" value="input.fasta"/> + <param name="equate_il" value="True"/> + <param name="extra" value="True"/> + <param name="names" value="True"/> + <param name="outputs" value="json,mismatch"/> + <output name="output_json"> + <assert_contents> + <has_text text="AIPQLEVARPADAYETAEAYR" /> + </assert_contents> + </output> + <output name="output_mismatch"> + <assert_contents> + <has_text text="DQIAHEGK" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + **Unipept** + + Retrieve Uniprot and taxanomic information for trypic peptides. + + **pept2prot** + 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. + + By default, each object contains the following information fields extracted from the UniProt record:: + + peptide: the peptide that matched this record + uniprot_id: the UniProt accession number of the matching record + taxon_id: the NCBI taxon id of the organism associated with the matching record + + When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt record:: + + taxon_name: the name of the organism associated with the matching UniProt record + ec_references: a space separated list of associated EC numbers + go_references: a space separated list of associated GO terms + refseq_ids: a space separated list of associated RefSeq accession numbers + refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers + insdc_ids: a space separated list of associated insdc accession numbers + insdc_protein_ids: a space separated list of associated insdc protein accession numbers + + http://unipept.ugent.be/apidocs/pept2prot + + **pept2taxa** + 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. + + By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: + + peptide: the peptide that matched this record + taxon_id: the NCBI taxon id of the organism associated with the matching record + taxon_name: the name of the organism associated with the matching record + taxon_rank: the taxonomic rank of the organism associated with the matching record + + 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:: + + superkingdom_id + kingdom_id + subkingdom_id + superphylum_id + phylum_id + subphylum_id + superclass_id + class_id + subclass_id + infraclass_id + superorder_id + order_id + suborder_id + infraorder_id + parvorder_id + superfamily_id + family_id + subfamily_id + tribe_id + subtribe_id + genus_id + subgenus_id + species_group_id + species_subgroup_id + species_id + subspecies_id + varietas_id + forma_id + + http://unipept.ugent.be/apidocs/pept2taxa + + **pept2lca** + 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. + + By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: + + peptide: the peptide that matched this record + taxon_id: the NCBI taxon id of the organism associated with the matching record + taxon_name: the name of the organism associated with the matching record + taxon_rank: the taxonomic rank of the organism associated with the matching record + + 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:: + + superkingdom_id + kingdom_id + subkingdom_id + superphylum_id + phylum_id + subphylum_id + superclass_id + class_id + subclass_id + infraclass_id + superorder_id + order_id + suborder_id + infraorder_id + parvorder_id + superfamily_id + family_id + subfamily_id + tribe_id + subtribe_id + genus_id + subgenus_id + species_group_id + species_subgroup_id + species_id + subspecies_id + varietas_id + forma_id + + http://unipept.ugent.be/apidocs/pept2lca + + **Attributions** + + The Unipept metaproteomics analysis pipeline + Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1 + Article first published online: 11 FEB 2015 + DOI: 10.1002/pmic.201400361 + http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400361/abstract;jsessionid=BFF1994E4C14DA73D7C907EB208AD710.f04t04 + + ]]></help> + <citations> + <citation type="doi">doi:10.1002/pmic.201400361</citation> + </citations> + +</tool>