# HG changeset patch
# User proteore
# Date 1580979770 18000
# Node ID b05fa99ddda28e91f611104430a183a2f260f1c9
# Parent  e967a99d66b3c3cc31a972c8b3f7ef182cf6e1f0
"planemo upload commit a23ff40d482d58e0425108bf60372e5fcafb847e"

diff -r e967a99d66b3 -r b05fa99ddda2 data_manager/resource_building.py
--- a/data_manager/resource_building.py	Thu Jan 23 08:38:02 2020 -0500
+++ b/data_manager/resource_building.py	Thu Feb 06 04:02:50 2020 -0500
@@ -48,6 +48,10 @@
         tissue_name = "HPA full atlas"
         url = "https://www.proteinatlas.org/download/proteinatlas.tsv.zip"
         table = "proteore_protein_full_atlas"
+    elif tissue == "HPA_RNA_tissue":
+        tissue_name = "HPA RNA tissue"
+        url = "https://www.proteinatlas.org/download/rna_tissue_consensus.tsv.zip"
+        table = "proteore_protein_atlas_rna_tissue"
     
     output_file = tissue +"_"+ time.strftime("%d-%m-%Y") + ".tsv"
     path = os.path.join(target_directory, output_file)
diff -r e967a99d66b3 -r b05fa99ddda2 data_manager/resource_building.xml
--- a/data_manager/resource_building.xml	Thu Jan 23 08:38:02 2020 -0500
+++ b/data_manager/resource_building.xml	Thu Feb 06 04:02:50 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.01.21" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.02.06" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
@@ -45,6 +45,7 @@
                 <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_RNA_tissue">RNA Tissue</option>
             </param>
         </when>
         <when value="peptide_atlas">
diff -r e967a99d66b3 -r b05fa99ddda2 data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Jan 23 08:38:02 2020 -0500
+++ b/data_manager_conf.xml	Thu Feb 06 04:02:50 2020 -0500
@@ -31,6 +31,21 @@
                 </column>
             </output>
         </data_table>
+        <data_table name="proteore_protein_atlas_rna_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/${release}.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"/>
diff -r e967a99d66b3 -r b05fa99ddda2 tool-data/proteore_protein_atlas_rna_tissue.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/proteore_protein_atlas_rna_tissue.loc.sample	Thu Feb 06 04:02:50 2020 -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>	<release>   <name> <tissue>	<value>
+#9979819281	HPA_RNA_tissue_19-07-2018	HPA RNA tissue 19/07/2018	HPA_rna_tissue	/projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19159/dataset_39307_files/HPA_rna_tissue_19-07-2018.tsv
diff -r e967a99d66b3 -r b05fa99ddda2 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Thu Jan 23 08:38:02 2020 -0500
+++ b/tool_data_table_conf.xml.sample	Thu Feb 06 04:02:50 2020 -0500
@@ -8,6 +8,10 @@
     <columns>id, release, name, tissue, value</columns>
     <file path="tool-data/proteore_protein_atlas_normal_tissue.loc" />
   </table>
+  <table name="proteore_protein_atlas_rna_tissue" comment_char="#">
+    <columns>id, release, name, tissue, value</columns>
+    <file path="tool-data/proteore_protein_atlas_rna_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" />