# HG changeset patch
# User proteore
# Date 1551880386 18000
# Node ID 0915249b8c4b6bd856e158ca40b1c36dd5606ba2
# Parent  0a26460d736645bc61c791baa39ed93ed32283b2
planemo upload commit 4dd1a2f7d196a1d2e70fab379a2c08367da0fe94-dirty

diff -r 0a26460d7366 -r 0915249b8c4b data_manager/resource_building.py
--- a/data_manager/resource_building.py	Mon Mar 04 05:03:04 2019 -0500
+++ b/data_manager/resource_building.py	Wed Mar 06 08:53:06 2019 -0500
@@ -39,12 +39,15 @@
     if tissue == "HPA_normal_tissue":
         tissue_name = "HPA normal tissue"
         url = "https://www.proteinatlas.org/download/normal_tissue.tsv.zip"
+        table = "proteore_protein_atlas_normal_tissue"
     elif tissue == "HPA_pathology":
         tissue_name = "HPA pathology"
         url = "https://www.proteinatlas.org/download/pathology.tsv.zip"
+        table = "proteore_protein_atlas_tumor_tissue"
     elif tissue == "HPA_full_atlas":
         tissue_name = "HPA full atlas"
         url = "https://www.proteinatlas.org/download/proteinatlas.tsv.zip"
+        table = "proteore_protein_full_atlas"
     
     output_file = tissue +"_"+ time.strftime("%d-%m-%Y") + ".tsv"
     path = os.path.join(target_directory, output_file)
@@ -52,8 +55,9 @@
     tissue_name = tissue_name + " " + time.strftime("%d/%m/%Y")
     tissue_id = tissue_name.replace(" ","_").replace("/","-")
 
+
     data_table_entry = dict(id=tissue_id, name = tissue_name, tissue = tissue, value = path)
-    _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_protein_atlas")
+    _add_data_table_entry(data_manager_dict, data_table_entry, table)
 
 
 #######################################################################################################
@@ -228,7 +232,7 @@
     id = species+"_id_mapping_"+ time.strftime("%d-%m-%Y")
 
     data_table_entry = dict(id=id, name = name, value = species, path = path)
-    _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_id_mapping")
+    _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_idmapping_"+species)
 
 def download_from_uniprot_ftp(file,target_directory) :
     ftp_dir = "pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/"
diff -r 0a26460d7366 -r 0915249b8c4b data_manager/resource_building.xml
--- a/data_manager/resource_building.xml	Mon Mar 04 05:03:04 2019 -0500
+++ b/data_manager/resource_building.xml	Wed Mar 06 08:53:06 2019 -0500
@@ -1,8 +1,9 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.04" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.06" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
 <requirements>
+    <!--requirement type="package" version="1.8.2">sparqlwrapper</requirement-->
 </requirements>
 <stdio>
   <exit_code range="1:" />
@@ -39,7 +40,7 @@
             <param name="tissues" type="select" multiple="false" label="Please select tissue">
                 <option value="HPA_normal_tissue">Normal tissue</option>
                 <option value="HPA_pathology">Pathology</option>
-                <option value="HPA_full_atlas">Full Atlas</option>
+                <!--option value="HPA_full_atlas">Full Atlas</option-->
             </param>
         </when>
         <when value="peptide_atlas">
diff -r 0a26460d7366 -r 0915249b8c4b data_manager_conf.xml
--- a/data_manager_conf.xml	Mon Mar 04 05:03:04 2019 -0500
+++ b/data_manager_conf.xml	Wed Mar 06 08:53:06 2019 -0500
@@ -1,7 +1,21 @@
 <?xml version="1.0"?>
 <data_managers>
     <data_manager tool_file="data_manager/resource_building.xml" id="resource_building">
-        <data_table name="proteore_protein_atlas">
+        <data_table name="proteore_protein_atlas_normal_tissue">
+            <output>
+                <column name="id"/>
+                <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/${id}.tsv</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+        <data_table name="proteore_protein_atlas_tumor_tissue">
             <output>
                 <column name="id"/>
                 <column name="name" />
@@ -30,7 +44,37 @@
                 </column>
             </output>
         </data_table>
-        <data_table name="proteore_id_mapping">
+        <data_table name="proteore_id_mapping_Human">
+            <output>
+                <column name="id" />
+                <column name="name" />
+                <column name="value" />
+                <column name="path" output_ref="output" >
+                    <move type="file">
+                        <!--source>${path}</source-->
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+        <data_table name="proteore_id_mapping_Mouse">
+            <output>
+                <column name="id" />
+                <column name="name" />
+                <column name="value" />
+                <column name="path" output_ref="output" >
+                    <move type="file">
+                        <!--source>${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 type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+        <data_table name="proteore_id_mapping_Rat">
             <output>
                 <column name="id" />
                 <column name="name" />
diff -r 0a26460d7366 -r 0915249b8c4b tool-data/proteore_id_mapping.loc.sample
--- a/tool-data/proteore_id_mapping.loc.sample	Mon Mar 04 05:03:04 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#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
-#mouse_id_mapping_01-01-2018	Mouse (Mus musculus)	mouse_id_mapping	tool-data/mouse_id_mapping.tsv
-#rat_id_mapping_01-01-2018	Rat (Rattus norvegicus)	rat_id_mapping	tool-data/rat_id_mapping.tsv
diff -r 0a26460d7366 -r 0915249b8c4b tool-data/proteore_id_mapping_Human.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/proteore_id_mapping_Human.loc.sample	Wed Mar 06 08:53:06 2019 -0500
@@ -0,0 +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
diff -r 0a26460d7366 -r 0915249b8c4b tool-data/proteore_id_mapping_Mouse.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/proteore_id_mapping_Mouse.loc.sample	Wed Mar 06 08:53:06 2019 -0500
@@ -0,0 +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
diff -r 0a26460d7366 -r 0915249b8c4b tool-data/proteore_id_mapping_Rat.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/proteore_id_mapping_Rat.loc.sample	Wed Mar 06 08:53:06 2019 -0500
@@ -0,0 +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
diff -r 0a26460d7366 -r 0915249b8c4b tool-data/proteore_protein_atlas.loc.sample
--- a/tool-data/proteore_protein_atlas.loc.sample	Mon Mar 04 05:03:04 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-#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
-#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
-#HPA_full_atlas_19-07-2018	HPA full atlas 19/07/2018	HPA_full_atlas	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19161/dataset_39309_files/HPA_full_atlas_19-07-2018.tsv
diff -r 0a26460d7366 -r 0915249b8c4b tool-data/proteore_protein_atlas_normal_tissue.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/proteore_protein_atlas_normal_tissue.loc.sample	Wed Mar 06 08:53:06 2019 -0500
@@ -0,0 +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
diff -r 0a26460d7366 -r 0915249b8c4b tool-data/proteore_protein_atlas_tumor_tissue.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/proteore_protein_atlas_tumor_tissue.loc.sample	Wed Mar 06 08:53:06 2019 -0500
@@ -0,0 +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
diff -r 0a26460d7366 -r 0915249b8c4b tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Mar 04 05:03:04 2019 -0500
+++ b/tool_data_table_conf.xml.sample	Wed Mar 06 08:53:06 2019 -0500
@@ -4,13 +4,25 @@
       <columns>id, name, tissue, value</columns>
       <file path="tool-data/proteore_peptide_atlas.loc"/>
     </table>
-    <table name="proteore_protein_atlas" comment_char="#">
+    <table name="proteore_protein_atlas_normal_tissue" comment_char="#">
       <columns>id, name, tissue, value</columns>
-      <file path="tool-data/proteore_protein_atlas.loc" />
+      <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" comment_char="#">
+    <table name="proteore_id_mapping_Human" comment_char="#">
+      <columns>id, name, value, path</columns>
+      <file path="tool-data/proteore_id_mapping_Human.loc" />
+    </table>
+    <table name="proteore_id_mapping_Mouse" comment_char="#">
       <columns>id, name, value, path</columns>
-      <file path="tool-data/proteore_id_mapping.loc" />
+      <file path="tool-data/proteore_id_mapping_Mouse.loc" />
+    </table>
+    <table name="proteore_id_mapping_Rat" comment_char="#">
+      <columns>id, name, value, path</columns>
+      <file path="tool-data/proteore_id_mapping_Rat.loc" />
     </table>
     <table name="proteore_biogrid_dictionaries" comment_char="#">
       <columns>id, name, species, value</columns>