# HG changeset patch
# User proteore
# Date 1557475163 14400
# Node ID aca66c3b8fbbf6c636fbe82de9e00cb0f3ab80e8
# Parent  69c70e45d5ab14a58e4b7020d42bf56e528d1122
planemo upload commit 3e8aad84b7fe9218370364b1aef3ea5779475f9f-dirty

diff -r 69c70e45d5ab -r aca66c3b8fbb add_protein_features.R
--- a/add_protein_features.R	Mon Mar 11 04:48:52 2019 -0400
+++ b/add_protein_features.R	Fri May 10 03:59:23 2019 -0400
@@ -194,7 +194,7 @@
     res = res[!duplicated(res$NextprotID),]
     output_content = merge(file, res,by.x=ncol,by.y="NextprotID",incomparables = NA,all.x=T)
     output_content = order_columns(output_content,ncol,id_type,file)
-    output_content = output_content[,-which(colnames(output_content)=="NextprotID")]      #remove nextprotID column
+    if (id_type=="Uniprot_AC"){output_content = output_content[,-which(colnames(output_content)=="NextprotID")]}      #remove nextprotID column
     output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" et " " to NA
     write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
   } 
diff -r 69c70e45d5ab -r aca66c3b8fbb add_protein_features.xml
--- a/add_protein_features.xml	Mon Mar 11 04:48:52 2019 -0400
+++ b/add_protein_features.xml	Fri May 10 03:59:23 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="prot_features" name="Add protein features" version="2019.03.11">
+<tool id="prot_features" name="Add protein features" version="2019.05.10">
 <description>[neXtProt]
 </description>
 <requirements>
@@ -24,7 +24,7 @@
   --diseases_info='$Nextprot_params.diseases_info'  
   --output='$output'  
 
-  #if 'nextprot_ref' in str($ref_file).split("/")
+  #if 'proteore_nextprot_ref' in str($ref_file).split("/")
     --nextprot="$ref_file" 
   #else 
     --nextprot="$__tool_directory__/$ref_file"
@@ -81,11 +81,13 @@
  		      <option value="SubcellLocations" selected="false">Subcellular Location</option>
         </param>
 
-        <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" />
+        <param name="diseases_info" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Disease information" />
 
       </section>
       <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
-        <options from_data_table="proteore_nextprot_ref"/>
+        <options from_data_table="proteore_nextprot_ref">
+            <filter type="sort_by" column="1"/>
+        </options>
       </param>
 
 </inputs>
diff -r 69c70e45d5ab -r aca66c3b8fbb proteore_nextprot_ref.loc.sample
--- a/proteore_nextprot_ref.loc.sample	Mon Mar 11 04:48:52 2019 -0400
+++ b/proteore_nextprot_ref.loc.sample	Fri May 10 03:59:23 2019 -0400
@@ -1,2 +1,3 @@
-#<id>	<name>	<value>
-nextprot_ref_09-03-2019	neXtProt release 09-03-2019	tool-data/nextprot_ref_09-03-2019.tsv
+#<id>	<release>	<name>	<value>
+9979818992	nextprot_ref_08-10-2018	neXtProt release 08-10-2018	tool-data/nextprot_ref_08-10-2018.tsv
+9979809691	nextprot_ref_09-03-2019	neXtProt release 09-03-2019	tool-data/nextprot_ref_09-03-2019.tsv
diff -r 69c70e45d5ab -r aca66c3b8fbb tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Mar 11 04:48:52 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Fri May 10 03:59:23 2019 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tables>
     <table name='proteore_nextprot_ref' comment_char="#">
-      <columns>id, name, value</columns>
+      <columns>id, release, name, value</columns>
       <file path="tool-data/proteore_nextprot_ref.loc"/>
     </table>
 </tables>