# HG changeset patch
# User proteore
# Date 1576255953 0
# Node ID 1ace270da46c2bb52b2c89370511f9a2d087365e
# Parent  9da22aba28bf8d59dc4f982e094f63a5e1210f72
planemo upload commit c9d70181a2b587e53dcc4b5885b74b625def6b8c-dirty

diff -r 9da22aba28bf -r 1ace270da46c add_protein_features_3orga.R
--- a/add_protein_features_3orga.R	Fri Dec 13 15:38:24 2019 +0000
+++ b/add_protein_features_3orga.R	Fri Dec 13 16:52:33 2019 +0000
@@ -177,6 +177,7 @@
     uniprot_file <- read.table(args$uniprot_file_human, header = TRUE , sep = "\t", fill = TRUE,stringsAsFactors = FALSE, quote="", check.names = F, comment.char = "")
   } else if (org=="Rat") {
     uniprot_file <- read.table(args$uniprot_file_rat, header = TRUE , sep = "\t", fill = TRUE,stringsAsFactors = FALSE, quote="", check.names = F, comment.char = "")
+  }
 
   # Parse arguments
   pc_features = gsub("__ob__","[",gsub("__cb__","]",strsplit(args$pc_features, ",")[[1]]))
diff -r 9da22aba28bf -r 1ace270da46c add_protein_features_3orga.xml
--- a/add_protein_features_3orga.xml	Fri Dec 13 15:38:24 2019 +0000
+++ b/add_protein_features_3orga.xml	Fri Dec 13 16:52:33 2019 +0000
@@ -1,4 +1,4 @@
-<tool id="prot_features_3orga" name="Add protein features (3 orga)" version="2019.12.13.1">
+<tool id="prot_features_3orga" name="Add protein features (3 orga)" version="2019.12.13.2">
 <description>[UniProt]
 </description>
 <requirements>
@@ -12,9 +12,7 @@
   Rscript $__tool_directory__/add_protein_features_3orga.R 
   --inputtype="$inputtype.filetype"
   --input='$inputtype.genelist'
-  --org='$org'
-
-
+  
   #if $inputtype.filetype == "file" 
     --column='$inputtype.column' 
     --header=$inputtype.header
@@ -23,6 +21,7 @@
     --output='$output2'
   #end if
 
+  --org='$org'
   --pc_features='$pc_features'   
   --uniprot_file_mouse=$__tool_directory__/tool-data/uniprot_features_mouse.tsv 
   --uniprot_file_human=$__tool_directory__/tool-data/uniprot_features_human.tsv  
@@ -62,11 +61,11 @@
     </when>
   </conditional>
 
-    <param name="org" type="select" label="Species (Human, Mouse, Rat)">
-      <option value="Human" selected="true">Human (Homo sapiens)</option>
-      <option value="Mouse">Mouse (Mouse musculus)</option>
-      <option value="Rat">Rat (Rattus norvegicus)</option>
-    </param>
+  <param name="org" type="select" label="Species (Human, Mouse, Rat)">
+    <option value="Human" selected="true">Human (Homo sapiens)</option>
+    <option value="Mouse">Mouse (Mouse musculus)</option>
+    <option value="Rat">Rat (Rattus norvegicus)</option>
+  </param>
 
     <param name="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="false">
       <option value="Entry name" selected="false">Entry name (e.g. PLK3_MOUSE)</option>