diff kegg_maps_visualization.xml @ 10:a4db9efe1e43 draft

"planemo upload commit 78a50fa16dcea6afd93a2f4de17ed193a2aa7dd3-dirty"
author proteore
date Mon, 02 Mar 2020 09:23:05 +0000
parents 9ac0ade20b3f
children 7d04efde2526
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--- a/kegg_maps_visualization.xml	Wed Jan 08 09:03:41 2020 +0000
+++ b/kegg_maps_visualization.xml	Mon Mar 02 09:23:05 2020 +0000
@@ -1,9 +1,10 @@
-<tool id="kegg_maps_visualization" name="Pathways visualization" version="2020.01.08">
-    <description>of (differentially expressed) genes/proteins [KEGG]</description>
+<tool id="kegg_maps_visualization" name="KEGG pathways mapping and visualization" version="2020.03.02">
+    <description>[PathView]</description>
     <requirements>
         <requirement type="package" version="3.6.2" >R</requirement>
         <requirement type="package" version="1.26.0">bioconductor-pathview</requirement>
         <requirement type="package" version="1.26.0">bioconductor-keggrest</requirement>
+        <requirement type="package" version="1.30.10">r-biocmanager</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         Rscript $__tool_directory__/kegg_maps_visualization.R 
@@ -261,6 +262,11 @@
 2. "Select ID type for genes to map on the pathway(s)": Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number. IDs to be mapped can be either provided by copy/paste or a file (tabular, tsv, txt) with a column containing the IDs. 
 3. "Map quantitative data on the pathway ?": Yes/No (default is No). Fold change values (up to three columns) from a dataset (same file as identifiers to map) can be graphically represented on the final figure (using a range of color representing the fold-change values).
 
+.. class:: warningmark 
+
+Some pathway ids causes error with the KEGG API: **hsa04215**, **mmu04723**. These ids will not be used if present in input.
+
+
 Below is an example of an input file with identifiers (uniprot_AC) and fold_change values.
 
 .. csv-table:: Simulated data