Mercurial > repos > proteore > proteore_compute_kegg_pathways

changeset 3:0d5c21cc29f7 draft

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planemo upload commit 0be58bb700f64de6792a7234a11675bae2755e8f-dirty
author proteore
date Thu, 13 Sep 2018 03:24:24 -0400
parents 39d3478fbc5e
children 7d8848c4dbb7
files compute_kegg_pathways.R compute_kegg_pathways.xml entrez_kegg_list.loc.sample uniprot_kegg_list.loc.sample
diffstat 4 files changed, 9 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/compute_kegg_pathways.R	Fri Sep 07 10:21:21 2018 -0400
+++ b/compute_kegg_pathways.R	Thu Sep 13 03:24:24 2018 -0400
@@ -88,7 +88,7 @@
     
     res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)]))
     res <- res[order(as.numeric(res[,3]),decreasing = TRUE),]
-    colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"# genes mapped in the pathway", "# total genes present in the pathway")
+    colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb genes mapped in the pathway", "nb total genes present in the pathway")
     
     return(res)
     
--- a/compute_kegg_pathways.xml	Fri Sep 07 10:21:21 2018 -0400
+++ b/compute_kegg_pathways.xml	Thu Sep 13 03:24:24 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="compute_kegg_pathways" name="Compute KEGG pathways coverage using KEGG REST api" version="2018.09.07">
+<tool id="compute_kegg_pathways" name="Compute KEGG pathways coverage using KEGG REST api" version="2018.09.13">
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
     </requirements>
@@ -88,9 +88,9 @@
 
 * **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970)
 * **Description:** name of the pathway as in KEGG
-* **Ratio IDs mapped/total IDs (% ):** percentage of pathway coverage
-* **'#' mapped IDs:** number of genes/proteins of your list mapped on the KEGG pathway
-* **'#' total IDs:** total number of genes/proteins present in the KEGG pathway
+* **Ratio IDs mapped/total IDs (%):** percentage of pathway coverage
+* **nb genes mapped in the pathway:** number of genes/proteins of your list mapped on the KEGG pathway
+* **nb total genes present in the pathway:** total number of genes/proteins present in the KEGG pathway
 
 -----
 
--- a/entrez_kegg_list.loc.sample	Fri Sep 07 10:21:21 2018 -0400
+++ b/entrez_kegg_list.loc.sample	Thu Sep 13 03:24:24 2018 -0400
@@ -1,3 +1,3 @@
 #name	date	organism	value(path)
-Human	27-07-18	hsa	tool-data/l.hsa.gene.RData
-Mouse	27-07-18	mmu	tool-data/l.mmu.gene.RData
+Human (Homo sapiens)	27-07-18	hsa	tool-data/l.hsa.gene.RData
+Mouse (Mus musculus)	27-07-18	mmu	tool-data/l.mmu.gene.RData
--- a/uniprot_kegg_list.loc.sample	Fri Sep 07 10:21:21 2018 -0400
+++ b/uniprot_kegg_list.loc.sample	Thu Sep 13 03:24:24 2018 -0400
@@ -1,3 +1,3 @@
 #name	date	organism	value(path)
-Human	27-07-18	hsa	tool-data/l.hsa.up.RData
-Mouse	27-07-18	mmu	tool-data/l.mmu.up.RData
+Human (Homo sapiens)	27-07-18	hsa	tool-data/l.hsa.up.RData
+Mouse (Mus musculus)	27-07-18	mmu	tool-data/l.mmu.up.RData