Mercurial > repos > proteore > proteore_kegg_pathways_coverage

changeset 3:0308c2d81607 draft

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planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
author proteore
date Fri, 28 Jun 2019 05:15:49 -0400
parents 60368fca9772
children 1fb202eb3609
files kegg_identification.xml
diffstat 1 files changed, 9 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/kegg_identification.xml	Tue Mar 05 09:37:56 2019 -0500
+++ b/kegg_identification.xml	Fri Jun 28 05:15:49 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="kegg_identification" name="Pathways identification" version="2019.03.05">
+<tool id="kegg_identification" name="Pathways identification" version="2019.06.27">
     <description>and coverage [KEGG]</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
@@ -22,7 +22,7 @@
     ]]></command>
     <inputs>
         <conditional name="input" >
-            <param name="ids" type="select" label="Enter your IDs (Entrez gene IDs, KEGG gene IDs or UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" >
+            <param name="ids" type="select" label="Enter your IDs (Entrez gene IDs, KEGG IDs, UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" >
                 <option value="text">Copy/paste your IDs</option>
                 <option value="file" selected="true">Input file containing your IDs</option>
             </param>
@@ -93,9 +93,11 @@
 
 .. class:: warningmark  
 
-If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming.
+If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming. KEGG database being "gene-centric" we recommend the use of Entrez gene IDs.
 
-If your input file contains other type of ID, please use the ID_Converter tool.
+If your input file contains other type of ID (than those allowed), please use the ID_Converter tool.
+
+In copy/paste mode, the number of IDs considered in input is limited to 5000.
 
 -----
 
@@ -133,13 +135,13 @@
 
 **Galaxy integration**
 
-David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
-Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
+Sandra Dérozier, Olivier Rué, 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>