Mercurial > repos > proteore > proteore_prot_features
diff add_protein_features.xml @ 18:0a9ae3d7dbf2 draft default tip
"planemo upload commit 7afd4b3ee25f024257ccbac6e51076d25b2a04e7"
author | proteore |
---|---|
date | Thu, 20 Aug 2020 03:09:52 -0400 |
parents | 2952bae8a1ea |
children |
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--- a/add_protein_features.xml Fri Jan 24 05:04:15 2020 -0500 +++ b/add_protein_features.xml Thu Aug 20 03:09:52 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="prot_features" name="Add protein features" version="2020.01.23"> +<tool id="prot_features" name="Add protein features" version="2020.08.17"> <description>[neXtProt, Human] </description> <requirements> @@ -19,9 +19,7 @@ #end if --type='$idtype' - --pc_features='$Nextprot_params.pc_features' - --localization='$Nextprot_params.localization' - --diseases_info='$Nextprot_params.diseases_info' + --pc_features='$pc_features' --output='$output' #if 'proteore_nextprot_ref' in str($ref_file).split("/") @@ -63,32 +61,31 @@ </when> </conditional> - <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> - <option value="NextprotID" selected="true">neXtProt IDs</option> - <option value="Uniprot_AC" selected="false">UniProt accession number</option> - </param> - <section name="Nextprot_params" title="Select features (Physico-chemical, localization, disease infiormation)" expanded="True"> - <param name="pc_features" type="select" label="Select information to add to your list" multiple="true" help="" display="checkboxes" optional="false"> - <option value="SeqLength" selected="false">Sequence Length</option> - <option value="MW" selected="false">Molecular Weight</option> - <option value="IsoPoint" selected="false">Isoelectric point</option> - <option value="TMDomains" selected="false">Number of transmembrane domains</option> - <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option> - </param> + <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> + <option value="NextprotID" selected="true">neXtProt IDs</option> + <option value="Uniprot_AC" selected="false">UniProt accession number</option> + </param> + <param name="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="false"> + <option value="ProteinName" selected="false">Protein name</option> + <option value="SeqLength" selected="false">Sequence Length</option> + <option value="MW" selected="false">Molecular Weight</option> + <option value="IsoPoint" selected="false">Isoelectric point</option> + <option value="TMDomains" selected="false">Number of transmembrane domains</option> + <option value="SubcellLocations" selected="false">Subcellular Location</option> + <option value="Diseases" selected="false">Disease information</option> + <option value="Function" selected="false">Protein function</option> + <option value="PostTranslationalModifications" selected="false">Post translational modifications</option> + <option value="ProteinFamily" selected="false">Protein family</option> + <option value="Pathway" selected="false">Pathway(s)</option> + <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option> + <option value="Chr" selected="false">Chromosome</option> + </param> - <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true"> - <option value="Chr" selected="false">Chromosome</option> - <option value="SubcellLocations" selected="false">Subcellular Location</option> - </param> - - <param name="diseases_info" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Disease information" /> - - </section> - <param name="ref_file" type="select" label="Release of neXtProt reference file to use"> + <param name="ref_file" type="select" label="Release of neXtProt reference file to use"> <options from_data_table="proteore_nextprot_ref"> <filter type="sort_by" column="0"/> </options> - </param> + </param> </inputs> @@ -110,12 +107,7 @@ </conditional> <param name="idtype" value="Uniprot_AC"/> - - <section name="Nextprot_params"> - <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> - <param name="localization" value="Chr,SubcellLocations"/> - <param name="diseases_info" value="true"/> - </section> + <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> <param name="ref_file" value="test-data/cached_locally/nextprot_ref_07-05-2019.tsv"/> <output name="output" file="Add_information_from_neXtProt.tsv"/> @@ -126,7 +118,7 @@ **Description** -This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich your protein IDs list. +This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich and better inform your protein IDs list. ----- @@ -148,7 +140,11 @@ **Output** -Output is a tabular file containing both original columns and new columns including the annotation requested. +Output is a tabular file containing both original columns and new columns including the annotation requested. Only features/annotations assigned with a "GOLD" quality criterion are considered, otherwise a "NA" value is returned. + +.. class:: warningmark + +"Protein name","Protein function","Post translational modifications","Protein family","Pathway(s)" options will not work will releases older than 08/2020. ----- @@ -158,16 +154,21 @@ neXtProt releases : -- nextProt release 07-05-2019 (release Feb 13, 2019) -- neXtProt release 08-10-2018 (release Feb 21, 2018) +- nextProt release 31-07-2020 (release Feb, 2020) +- nextProt release 07-05-2019 (release Feb, 2019) +- neXtProt release 08-10-2018 (release Feb, 2018) +.. class:: warningmark + +For "Protein function", "Post translational modifications" and "Pathway(s)", only results with gold quality are returned. + ----- .. class:: infomark **Authors** -David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +David Christiany, Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR