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author | proteore |
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date | Wed, 21 Mar 2018 10:49:19 -0400 |
parents | fc0118aa432a |
children | 2e53ba3b1697 |
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<tool id="prot_features" name="Protein features" version="0.1.0"> <description> add biochemical and cellular annotation to your protein list from neXtProt </description> <requirements> <requirement type="package" version="3.4.1">R</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ #if $inputtype.filetype == "copy_paste": Rscript $__tool_directory__/protein_features.R --inputtype=copypaste --input='$inputtype.genelist' --nextprot=$__tool_directory__/tool-data/result_nextprot.txt --column=c1 --header=None --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' #end if #if $inputtype.filetype == "file_all": Rscript $__tool_directory__/protein_features.R --inputtype=tabfile --input='$inputtype.genelist' --nextprot=$__tool_directory__/tool-data/result_nextprot.txt --column='$inputtype.column' --header='$inputtype.header' --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' #end if ]]></command> <inputs> <conditional name="inputtype"> <param name="filetype" type="select" label="Select your type of input file"> <option value="file_all">Input file containing your identifiers (neXtProt or Uniprot ID)</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 identifiers"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> </mapping> </sanitizer> </param> </when> <when value="file_all"> <param name="genelist" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="This file must imperatively have 1 column filled with IDs consistent with the neXtprot database (Uniprot accession number or neXtProt ID). If this is not the case, please use the ID_Converter tool."/> <param name="column" type="text" label="Please specify the column where are your IDs (e.g : Enter c1 for column n°1)" value="c1"/> <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> <option value="true" selected="true">Yes</option> <option value="false" selected="false">No</option> </param> </when> </conditional> <param name="idtype" type="select" label="Type of your input ids" multiple="false" optional="false"> <option value="uniprot" selected="true">Uniprot accession number</option> <option value="nextprot" selected="false">neXtProt IDs</option> </param> <section name="Nextprot_params" title="Select features of interest (compulsory step)" expanded="True"> <param name="P1" type="select" label="Physico-Chemical Features" multiple="true" help="Choose the information you want to add to your data from Nextprot" display="checkboxes" optional="true"> <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="P2" type="select" label="Localization" multiple="true" help="Choose the information you want to add to your data from Nextprot" display="checkboxes" optional="true"> <option value="Chr" selected="false">Chromosome</option> <option value="SubcellLocations" selected="false">Subcellular Location</option> </param> <param name="P3" type="select" label="Diseases information"> <option value="Diseases">Yes</option> <option value="None">No</option> </param> </section> </inputs> <outputs> <data name="output" format="tsv" label="Add information from neXtProt"/> </outputs> <tests> <test> <conditional name="inputtype"> <param name="filetype " value="tabfile"/> <param name="genelist" value="FKW_ID_Converter_Lacombe_et_al_2017_OK.txt"/> <param name="column" value="c1"/> <param name="header" value="true"/> </conditional> <param name="idtype" value="uniprot"/> <section name="Nextprot_params"> <param name="P1" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> <param name="P2" value="Chr,SubcellLocations"/> <param name="P3" value="Diseases"/> </section> <output name="output" file="Add_information_from_neXtProt.tsv"/> </test> </tests> <help><![CDATA[ This tool add annotation (protein features) from neXtProt database (knowledge base on human proteins) to your protein IDs list. **Input** Input can be a file containing multiple fields but 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. **Databases** Annotations have been retrieved from the neXtProt database released on 01/08/2017 (Gaudet et al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) **Outputs** The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected. **Authors** Lisa Peru, 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 This work has been partially funded through the French National Agency for Research (ANR) IFB project. Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. ]]></help> <citations> </citations> </tool>