Mercurial > repos > proteore > proteore_prot_features_mouse
changeset 2:1dea4e5f638f draft default tip
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
| author | proteore |
|---|---|
| date | Fri, 28 Jun 2019 05:05:58 -0400 |
| parents | f10816a9dd0b |
| children | |
| files | add_protein_features_mouse.R add_protein_features_mouse.xml |
| diffstat | 2 files changed, 13 insertions(+), 8 deletions(-) [+] |
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--- a/add_protein_features_mouse.R Mon Mar 04 05:12:46 2019 -0500 +++ b/add_protein_features_mouse.R Fri Jun 28 05:05:58 2019 -0400 @@ -11,6 +11,7 @@ } get_list_from_cp <-function(list){ + list = gsub(";","\t",list) list = strsplit(list, "[ \t\n]+")[[1]] list = gsub("NA","",list) list = list[list != ""] #remove empty entry
--- a/add_protein_features_mouse.xml Mon Mar 04 05:12:46 2019 -0500 +++ b/add_protein_features_mouse.xml Fri Jun 28 05:05:58 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="prot_features_mouse" name="Add protein features (Mouse)" version="2019.02.21"> +<tool id="prot_features_mouse" name="Add protein features (Mouse)" version="2019.06.27"> <description>[UniProt] </description> <requirements> @@ -105,21 +105,25 @@ **Description** -This tool retrieves annotation (protein features) from the UniProt database (Mouse proteins) to enrich your protein IDs list. +This tool retrieves annotation (protein features) from the UniProt database (Mouse reference proteome) to enrich your protein IDs list. ----- **Input** -A list of Uniprot Accession Number (e.g. P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number**. If your input file contains other type of IDs, please use the ID_Converter tool. +A list of UniProt Accession Number (e.g. P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number**. If your input file contains other type of IDs, please use the ID_Converter tool. + +.. class:: warningmark + +In copy/paste mode, the number of UniProt AccNumber considered in input, is limited to 5000. ----- **Parameters** -"Select features": three categories of annotation can be retrieved: physico-chemical features, localisation (chromosome, subcellular) and disease information (set to "Yes" by default). Select each feature according to your interest by clicking the corresponding checkbox. +"Select features": Select each feature according to your interest by clicking the corresponding checkbox. -You can get more information about annotations `here <https://www.uniprot.org/help/uniprotkb_column_names>`_. +for more information about these features click `here <https://www.uniprot.org/help/uniprotkb_column_names>`_. ----- @@ -133,7 +137,7 @@ **Data source (release date)** -Annotations have been retrieved from UniProt.org (02/2019). +Annotations have been retrieved from UniProt.org (release 02/2019). ----- @@ -141,13 +145,13 @@ **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 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: contact@proteore.org for any questions or concerns about this tool. ]]></help> <citations>