# HG changeset patch
# User proteore
# Date 1560933723 14400
# Node ID 9ec42cb35abd6d996b2ea83b37e6c21cee2e6f32
# Parent  f3507260b30f24b105b9435b6050bd703efbacf6
planemo upload commit 339ab77a83db03409c8001324f10b36ff5b13a39-dirty

diff -r f3507260b30f -r 9ec42cb35abd data_manager/resource_building.py
--- a/data_manager/resource_building.py	Tue Apr 16 07:46:59 2019 -0400
+++ b/data_manager/resource_building.py	Wed Jun 19 04:42:03 2019 -0400
@@ -53,10 +53,11 @@
     path = os.path.join(target_directory, output_file)
     unzip(url, path)    #download and save file
     tissue_name = tissue_name + " " + time.strftime("%d/%m/%Y")
-    tissue_id = tissue_name.replace(" ","_").replace("/","-")
+    release = tissue_name.replace(" ","_").replace("/","-")
+    id = str(10000000000 - int(time.strftime("%Y%m%d")))
 
 
-    data_table_entry = dict(id=tissue_id, name = tissue_name, tissue = tissue, value = path)
+    data_table_entry = dict(id=id, release=release, name = tissue_name, tissue = tissue, value = path)
     _add_data_table_entry(data_manager_dict, data_table_entry, table)
 
 
@@ -140,8 +141,6 @@
     if human : tab = [["UniProt-AC","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","neXtProt","BioGrid","STRING","KEGG"]]
     else : tab = [["UniProt-AC","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","BioGrid","STRING","KEGG"]]
 
-    #print("header ok")
-
     #get selected.tab and keep only ids of interest
     selected_tab_file=species_dict[species]+"_"+files[0]
     tab_path = download_from_uniprot_ftp(selected_tab_file,target_directory)
@@ -153,6 +152,21 @@
 
     #print("selected_tab ok")
 
+    #get uniprot-AC reviewed
+    organism = species_dict[species].split("_")[1]
+    query = "https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:"+organism+"&format=list"
+
+    with requests.Session() as s:
+        download = s.get(query)
+        decoded_content = download.content.decode('utf-8')
+        uniprot_reviewed_list = decoded_content.splitlines()
+
+    for line in tab[1:]:
+        UniProtAC = line[0]
+        if UniProtAC not in uniprot_reviewed_list :
+            line[0]=""
+            line[1]=""
+
     """
     Supplementary ID to get from HUMAN_9606_idmapping.dat :
     -NextProt,BioGrid,STRING,KEGG
@@ -204,7 +218,7 @@
 
     #print ("tab ok")
 
-    #add missing nextprot ID for human
+    #add missing nextprot ID for human or replace old ones
     if human : 
         #build next_dict
         nextprot_ids = id_list_from_nextprot_ftp("nextprot_ac_list_all.txt",target_directory)
@@ -217,7 +231,7 @@
         for line in tab[1:] : 
             uniprotID=line[0]
             nextprotID=line[13]
-            if nextprotID == '' and uniprotID in next_dict :
+            if uniprotID in next_dict and (nextprotID == '' or (nextprotID != "NX_"+uniprotID and next_dict[uniprotID] == "NX_"+uniprotID)) :
                 line[13]=next_dict[uniprotID]
 
     output_file = species+"_id_mapping_"+ time.strftime("%d-%m-%Y") + ".tsv"
@@ -229,9 +243,10 @@
 
     name_dict={"Human" : "Homo sapiens", "Mouse" : "Mus musculus", "Rat" : "Rattus norvegicus"}
     name = species +" (" + name_dict[species]+" "+time.strftime("%d/%m/%Y")+")"
-    id = species+"_id_mapping_"+ time.strftime("%d-%m-%Y")
+    release = species+"_id_mapping_"+ time.strftime("%d-%m-%Y")
+    id = str(10000000000 - int(time.strftime("%Y%m%d")))    #new ids must be inferior to previous id -> sort by <filter> in xml only in descending order
 
-    data_table_entry = dict(id=id, name = name, species = species, value = path)
+    data_table_entry = dict(id=id, release=release , name = name, species = species, value = path)
     _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_id_mapping_"+species)
 
 def download_from_uniprot_ftp(file,target_directory) :
@@ -483,15 +498,16 @@
         dico['protein_name']=dico_protein_name
 
     #writing output
-    output_file = species+'_'+interactome+'_'+ time.strftime("%d-%m-%Y") + ".json"
+    output_file = species+'_'+interactome+'_'+ time.strftime("%Y-%m-%d") + ".json"
     path = os.path.join(target_directory,output_file)
     name = species+" ("+species_dict[species]+") "+time.strftime("%d/%m/%Y")
-    id = species+"_"+interactome+"_"+ time.strftime("%d-%m-%Y")
+    release = species+"_"+interactome+"_"+ time.strftime("%Y-%m-%d")
+    id = str(10000000000 - int(time.strftime("%Y%m%d")))
 
     with open(path, 'w') as handle:
         json.dump(dico, handle, sort_keys=True)
 
-    data_table_entry = dict(id=id, name = name, species = species, value = path)
+    data_table_entry = dict(id=id, release=release, name = name, species = species, value = path)
     _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_"+interactome+"_dictionaries")
 
 #######################################################################################################
@@ -501,8 +517,18 @@
 def Build_nextprot_ref_file(data_manager_dict,target_directory):
     nextprot_ids_file = "nextprot_ac_list_all.txt"
     ids = id_list_from_nextprot_ftp(nextprot_ids_file,target_directory)
-
+    
+    output_file = 'nextprot_ref_'+ time.strftime("%d-%m-%Y") + ".tsv"
+    path = os.path.join(target_directory,output_file)
+    name = "neXtProt release "+time.strftime("%d-%m-%Y")
+    release_id = "nextprot_ref_"+time.strftime("%d-%m-%Y")
+    
+    output = open(path, 'w')
+    writer = csv.writer(output,delimiter="\t")
+        
     nextprot_file=[["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence"]]
+    writer.writerows(nextprot_file)
+    
     for id in ids :
         #print (id)
         query="https://api.nextprot.org/entry/"+id+".json"
@@ -547,21 +573,15 @@
             for tm in tm_domains :
                 all_tm_domains.add(tm['cvTermName'])
                 nb_domains+=1
-                print "nb domains ++"
-                print (nb_domains)
-
-    nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence])
-    
-    output_file = 'nextprot_ref_'+ time.strftime("%d-%m-%Y") + ".tsv"
-    path = os.path.join(target_directory,output_file)
-    name = "neXtProt release "+time.strftime("%d-%m-%Y")
-    id = "nextprot_ref_"+time.strftime("%d-%m-%Y")
-
-    with open(path, 'w') as output:
-        writer = csv.writer(output,delimiter="\t")
+                #print "nb domains ++"
+                #print (nb_domains)
+        nextprot_file[:] = [] 
+        nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence])
         writer.writerows(nextprot_file)
 
-    data_table_entry = dict(id=id, name = name, value = path)
+        id = str(10000000000 - int(time.strftime("%Y%m%d")))
+
+    data_table_entry = dict(id=id, release=release_id, name = name, value = path)
     _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_nextprot_ref")
 
 #######################################################################################################
diff -r f3507260b30f -r 9ec42cb35abd data_manager/resource_building.xml
--- a/data_manager/resource_building.xml	Tue Apr 16 07:46:59 2019 -0400
+++ b/data_manager/resource_building.xml	Wed Jun 19 04:42:03 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.04.04" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.06.13" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
@@ -94,6 +94,7 @@
                 <when value="humap"/>
             </conditional>
         </when>
+        <when value="nextprot"/>
     </conditional>
 </inputs>
 
diff -r f3507260b30f -r 9ec42cb35abd data_manager_conf.xml
--- a/data_manager_conf.xml	Tue Apr 16 07:46:59 2019 -0400
+++ b/data_manager_conf.xml	Wed Jun 19 04:42:03 2019 -0400
@@ -19,13 +19,14 @@
         <data_table name="proteore_protein_atlas_normal_tissue">
             <output>
                 <column name="id"/>
+                <column name="release"/>
                 <column name="name" />
                 <column name="tissue" />
                 <column name="value" output_ref="output" >
                     <move type="file">
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -33,13 +34,14 @@
         <data_table name="proteore_protein_atlas_tumor_tissue">
             <output>
                 <column name="id"/>
+                <column name="release"/>
                 <column name="name" />
                 <column name="tissue" />
                 <column name="value" output_ref="output" >
                     <move type="file">
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -47,6 +49,7 @@
         <data_table name="proteore_id_mapping_Human">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -54,7 +57,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -62,6 +65,7 @@
         <data_table name="proteore_id_mapping_Mouse">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -69,7 +73,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -77,6 +81,7 @@
         <data_table name="proteore_id_mapping_Rat">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -84,7 +89,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -92,6 +97,7 @@
         <data_table name="proteore_biogrid_dictionaries">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -99,7 +105,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -107,6 +113,7 @@
         <data_table name="proteore_bioplex_dictionaries">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -114,7 +121,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -122,6 +129,7 @@
         <data_table name="proteore_humap_dictionaries">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="species" />
                 <column name="value" output_ref="output" >
@@ -129,7 +137,7 @@
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
@@ -137,13 +145,14 @@
         <data_table name="proteore_nextprot_ref">
             <output>
                 <column name="id" />
+                <column name="release"/>
                 <column name="name" />
                 <column name="value" output_ref="output" >
                     <move type="file">
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">proteore_nextprot_ref/</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/proteore_nextprot_ref/${id}.tsv</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/proteore_nextprot_ref/${release}.tsv</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_biogrid_dictionaries.loc.sample
--- a/tool-data/proteore_biogrid_dictionaries.loc.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool-data/proteore_biogrid_dictionaries.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,4 +1,4 @@
-#id	name	species	value
-#biogrid_human_08-01-2019	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/Human_biogrid.json
-#biogrid_mouse_08-01-2019	Mouse (Mus musculus) 08/01/2019	Mouse	PPI_dictionaries/Mouse_biogrid.json
-#biogrid_rat_08-01-2019	Rat (Rattus norvegicus) 08/01/2019 Rat	PPI_dictionaries/Rat_biogrid.json
+#id	release name	species	value
+#9979809892	biogrid_human_2019-01-08	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/Human_biogrid.json
+#9979809892	biogrid_mouse_2019-01-08	Mouse (Mus musculus) 08/01/2019	Mouse	PPI_dictionaries/Mouse_biogrid.json
+#9979809892	biogrid_rat_2019-01-08	Rat (Rattus norvegicus) 08/01/2019 Rat	PPI_dictionaries/Rat_biogrid.json
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_bioplex_dictionaries.loc.sample
--- a/tool-data/proteore_bioplex_dictionaries.loc.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool-data/proteore_bioplex_dictionaries.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,2 +1,2 @@
-#id	name	species	value
-#bioplex_human_08-01-2019	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/human_bioplex.json
+#id	release name	species	value
+#9979809892	bioplex_human_2019-01-08	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/human_bioplex.json
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_humap_dictionaries.loc.sample
--- a/tool-data/proteore_humap_dictionaries.loc.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool-data/proteore_humap_dictionaries.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,2 +1,2 @@
-#id	name	species	value
-#humap_human_01-02-2019 Human (Homo sapiens) 01/02/19	Human	PPI_dictionaries/Human_humap_01-02-2019.json
+#id	release name	species	value
+#9979809799	humap_human_2019-01-02 Human (Homo sapiens) 01/02/19	Human	PPI_dictionaries/Human_humap_01-02-2019.json
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_id_mapping_Human.loc.sample
--- a/tool-data/proteore_id_mapping_Human.loc.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool-data/proteore_id_mapping_Human.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,3 +1,3 @@
 #This file lists the locations of reference file for id_converter tool
-#<id>	<name>	<value>	<path>
-#human_id_mapping_01-01-2018	Human (homo sapiens)	human_id_mapping	tool-data/human_id_mapping.tsv
+#<id>	<release>   <name>	<species>	<value>
+#9979818977	human_id_mapping_23-10-2018	Human (homo sapiens 23/10/2018)	Human	tool-data/human_id_mapping_23-10-2018.tsv
\ No newline at end of file
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_id_mapping_Mouse.loc.sample
--- a/tool-data/proteore_id_mapping_Mouse.loc.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool-data/proteore_id_mapping_Mouse.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,3 +1,3 @@
 #This file lists the locations of reference file for id_converter tool
-#<id>	<name>	<value>	<path>
-#mouse_id_mapping_01-01-2018	Mouse (Mus musculus)	mouse_id_mapping	tool-data/mouse_id_mapping.tsv
+#<id>	<release>   <name>	<species>	<value>
+#9979818977	mouse_id_mapping_23-10-2018	Mouse (Mus musculus 23-10-2018)	Mouse	tool-data/mouse_id_mapping_23-10-2018.tsv
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_id_mapping_Rat.loc.sample
--- a/tool-data/proteore_id_mapping_Rat.loc.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool-data/proteore_id_mapping_Rat.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,3 +1,3 @@
 #This file lists the locations of reference file for id_converter tool
-#<id>	<name>	<value>	<path>
-#rat_id_mapping_01-01-2018	Rat (Rattus norvegicus)	rat_id_mapping	tool-data/rat_id_mapping.tsv
+#<id>	<release>   <name>	<species>	<value>
+#9979818977	rat_id_mapping_23-10-2018	Rat (Rattus norvegicus 23-10-2018)	Rat	tool-data/rat_id_mapping_23-10-2018.tsv
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_nextprot_ref.loc.sample
--- a/tool-data/proteore_nextprot_ref.loc.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool-data/proteore_nextprot_ref.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,2 +1,2 @@
-#<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>
+#9979809691	nextprot_ref_09-03-2019	neXtProt release 09-03-2019	tool-data/nextprot_ref_09-03-2019.tsv
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_peptide_atlas.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/proteore_peptide_atlas.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -0,0 +1,10 @@
+#This file lists the locations name and values of reference files for number of MS/MS observations in a tissue
+#This is a tab separated file (TAB, not 4 spaces !)
+#<id>	<name>	<tissue>	<value>
+#Human_Heart_20-07-2018	Human Heart 20/07/2018	Human_Heart	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Heart_20-07-2018.tsv
+#Human_Liver_20-07-2018	Human Liver 20/07/2018	Human_Liver	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Liver_20-07-2018.tsv
+#Human_Urine_20-07-2018	Human Urine 20/07/2018	Human_Urine	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Urine_20-07-2018.tsv
+#Human_Brain_20-07-2018	Human Brain 20/07/2018	Human_Brain	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Brain_20-07-2018.tsv
+#Human_Kidney_20-07-2018	Human Kidney 20/07/2018	Human_Kidney	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Kidney_20-07-2018.tsv
+#Human_Plasma_20-07-2018	Human Plasma 20/07/2018	Human_Plasma	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Plasma_20-07-2018.tsv
+#Human_CSF_20-07-2018	Human CSF 20/07/2018	Human_CSF	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_CSF_20-07-2018.tsv
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_protein_atlas_normal_tissue.loc.sample
--- a/tool-data/proteore_protein_atlas_normal_tissue.loc.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool-data/proteore_protein_atlas_normal_tissue.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,4 +1,4 @@
 #This file lists the locations name and values of reference files for Get expression data tool
 #This is a tab separated file (TAB, not 4 spaces !)
-#<id>	<name> <tissue>	<value>
-#HPA_normal_tissue_19-07-2018	HPA normal tissue 19/07/2018	HPA_normal_tissue	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19159/dataset_39307_files/HPA_normal_tissue_19-07-2018.tsv
+#<id>	<release>   <name> <tissue>	<value>
+#9979819281	HPA_normal_tissue_19-07-2018	HPA normal tissue 19/07/2018	HPA_normal_tissue	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19159/dataset_39307_files/HPA_normal_tissue_19-07-2018.tsv
diff -r f3507260b30f -r 9ec42cb35abd tool-data/proteore_protein_atlas_tumor_tissue.loc.sample
--- a/tool-data/proteore_protein_atlas_tumor_tissue.loc.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool-data/proteore_protein_atlas_tumor_tissue.loc.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,4 +1,4 @@
 #This file lists the locations name and values of reference files for Get expression data tool
 #This is a tab separated file (TAB, not 4 spaces !)
-#<id>	<name> <tissue>	<value>
-#HPA_pathology_19-07-2018	HPA pathology 19/07/2018	HPA_pathology	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19160/dataset_39308_files/HPA_pathology_19-07-2018.tsv
+#<id>	<release>	<name> <tissue>	<value>
+#9979819281	HPA_pathology_19-07-2018	HPA pathology 19/07/2018	HPA_pathology	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19160/dataset_39308_files/HPA_pathology_19-07-2018.tsv
diff -r f3507260b30f -r 9ec42cb35abd tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Tue Apr 16 07:46:59 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Wed Jun 19 04:42:03 2019 -0400
@@ -1,43 +1,43 @@
 <?xml version="1.0"?>
 <tables>
-    <table name='proteore_peptide_atlas' comment_char="#">
-      <columns>id, name, tissue, value</columns>
-      <file path="tool-data/proteore_peptide_atlas.loc"/>
-    </table>
-    <table name="proteore_protein_atlas_normal_tissue" comment_char="#">
-      <columns>id, name, tissue, value</columns>
-      <file path="tool-data/proteore_protein_atlas_normal_tissue.loc" />
-    </table>
-    <table name="proteore_protein_atlas_tumor_tissue" comment_char="#">
-      <columns>id, name, tissue, value</columns>
-      <file path="tool-data/proteore_protein_atlas_tumor_tissue.loc" />
-    </table>
-    <table name="proteore_id_mapping_Human" comment_char="#">
-      <columns>id, name, species, value</columns>
-      <file path="tool-data/proteore_id_mapping_Human.loc" />
-    </table>
-    <table name="proteore_id_mapping_Mouse" comment_char="#">
-      <columns>id, name, species, value</columns>
-      <file path="tool-data/proteore_id_mapping_Mouse.loc" />
-    </table>
-    <table name="proteore_id_mapping_Rat" comment_char="#">
-      <columns>id, name, species, value</columns>
-      <file path="tool-data/proteore_id_mapping_Rat.loc" />
-    </table>
-    <table name="proteore_biogrid_dictionaries" comment_char="#">
-      <columns>id, name, species, value</columns>
-      <file path="tool-data/proteore_biogrid_dictionaries.loc" />
-    </table>
-    <table name="proteore_bioplex_dictionaries" comment_char="#">
-      <columns>id, name, species, value</columns>
-      <file path="tool-data/proteore_bioplex_dictionaries.loc" />
-    </table>
-    <table name="proteore_humap_dictionaries" comment_char="#">
-      <columns>id, name, species, value</columns>
-      <file path="tool-data/proteore_humap_dictionaries.loc" />
-    </table>
-    <table name='proteore_nextprot_ref' comment_char="#">
-      <columns>id, name, value</columns>
-      <file path="tool-data/proteore_nextprot_ref.loc"/>
-    </table>
+  <table name="proteore_peptide_atlas" comment_char="#">
+    <columns>id, name, tissue, value</columns>
+    <file path="tool-data/proteore_peptide_atlas.loc"/>
+  </table>
+  <table name="proteore_protein_atlas_normal_tissue" comment_char="#">
+    <columns>id, release, name, tissue, value</columns>
+    <file path="tool-data/proteore_protein_atlas_normal_tissue.loc" />
+  </table>
+  <table name="proteore_protein_atlas_tumor_tissue" comment_char="#">
+    <columns>id, release, name, tissue, value</columns>
+    <file path="tool-data/proteore_protein_atlas_tumor_tissue.loc" />
+  </table>
+  <table name="proteore_id_mapping_Human" comment_char="#">
+    <columns>id, release, name, species, value</columns>
+    <file path="tool-data/proteore_id_mapping_Human.loc" />
+  </table>
+  <table name="proteore_id_mapping_Mouse" comment_char="#">
+    <columns>id, release, name, species, value</columns>
+    <file path="tool-data/proteore_id_mapping_Mouse.loc" />
+  </table>
+  <table name="proteore_id_mapping_Rat" comment_char="#">
+    <columns>id, release, name, species, value</columns>
+    <file path="tool-data/proteore_id_mapping_Rat.loc" />
+  </table>
+  <table name="proteore_biogrid_dictionaries" comment_char="#">
+    <columns>id, release, name, species, value</columns>
+    <file path="tool-data/proteore_biogrid_dictionaries.loc" />
+  </table>
+  <table name="proteore_bioplex_dictionaries" comment_char="#">
+    <columns>id, release, name, species, value</columns>
+    <file path="tool-data/proteore_bioplex_dictionaries.loc" />
+  </table>
+  <table name="proteore_humap_dictionaries" comment_char="#">
+    <columns>id, release, name, species, value</columns>
+    <file path="tool-data/proteore_humap_dictionaries.loc" />
+  </table>
+  <table name='proteore_nextprot_ref' comment_char="#">
+    <columns>id, release, name, value</columns>
+    <file path="tool-data/proteore_nextprot_ref.loc"/>
+  </table>
 </tables>