Mercurial > repos > proteore > proteore_prot_features
view add_protein_features.xml @ 18:0a9ae3d7dbf2 draft default tip
"planemo upload commit 7afd4b3ee25f024257ccbac6e51076d25b2a04e7"
author | proteore |
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date | Thu, 20 Aug 2020 03:09:52 -0400 |
parents | 2952bae8a1ea |
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<tool id="prot_features" name="Add protein features" version="2020.08.17"> <description>[neXtProt, Human] </description> <requirements> <requirement type="package" version="3.4.1">R</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ Rscript $__tool_directory__/add_protein_features.R --inputtype="$inputtype.filetype" --input='$inputtype.genelist' #if $inputtype.filetype == "file" --column='$inputtype.column' --header=$inputtype.header #end if --type='$idtype' --pc_features='$pc_features' --output='$output' #if 'proteore_nextprot_ref' in str($ref_file).split("/") --nextprot="$ref_file" #else --nextprot="$__tool_directory__/$ref_file" #end if ]]></command> <inputs> <conditional name="inputtype"> <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt; e.g. NX_P05090 or P05090)" help="Copy/paste or from a file" > <option value="file" selected="true">Input file containing your IDs </option> <option value="copy_paste">Copy/paste your list of IDs</option> </param> <when value="copy_paste"> <param name="genelist" type="text" label="Enter a list of IDs separated by tab, space or carriage return into the form field" help="for example : A0AVI2 A6NGB0"> <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value="'"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> <add source=" " target=""/> <add source="
" target=""/> <add source="
" target=""/> <add source="	" target=""/> </mapping> </sanitizer> </param> </when> <when value="file"> <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/> <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1"> <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> </param> <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" /> </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> <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="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> </inputs> <outputs> <data name="output" format="tsv" label="Add_information_from_neXtProt on ${inputtype.genelist.name}"> <filter>inputtype=="file"</filter> </data> <data name="output" format="tsv" label="Add_information_from_neXtProt"/> </outputs> <tests> <test> <conditional name="inputtype"> <param name="filetype" value="file"/> <param name="genelist" value="Lacombe_et_al_2017.tsv"/> <param name="column" value="c1"/> <param name="header" value="true"/> </conditional> <param name="idtype" value="Uniprot_AC"/> <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"/> </test> </tests> <help><![CDATA[ **Description** This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich and better inform your protein IDs list. ----- **Input** A list of of Uniprot Accession Number (e.g. P05090) or neXtProt IDs (e.g. NX_P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number or neXtProt IDs**. If your input file contains other type of IDs, please use the ID_Converter tool. .. class:: warningmark In copy/paste mode, the number of IDs considered in input is limited to 5000. ----- **Parameters** "Select features": select each feature of your interest by clicking the corresponding checkbox. Disease information is set to "Yes" by default. ----- **Output** 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. ----- **Data source (release date)** Annotations have been retrieved using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017) neXtProt releases : - 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 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 This work has been partially funded through the French National Agency for Research (ANR) IFB project. Help: contact@proteore.org for any questions or concerns about this tool. ]]></help> <citations> </citations> </tool>