Mercurial > repos > proteore > proteore_data_manager

changeset 46:e09edc8b1c90 draft

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"planemo upload commit 6bef056b0e52bfa39dbe8591bfe67f8c95bf3ba2-dirty"
author proteore
date Tue, 21 Jan 2020 16:18:05 +0000
parents 488e015576bc
children f89ddc972ad4
files data_manager/resource_building.xml data_manager_conf.xml tool_data_table_conf.xml.sample
diffstat 3 files changed, 20 insertions(+), 1 deletions(-) [+]
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line diff
--- a/data_manager/resource_building.xml	Wed Jan 08 15:15:16 2020 +0000
+++ b/data_manager/resource_building.xml	Tue Jan 21 16:18:05 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.01.08.14" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.01.21" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
--- a/data_manager_conf.xml	Wed Jan 08 15:15:16 2020 +0000
+++ b/data_manager_conf.xml	Tue Jan 21 16:18:05 2020 +0000
@@ -46,6 +46,21 @@
                 </column>
             </output>
         </data_table>
+        <data_table name="proteore_protein_full_atlas">
+            <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_id_mapping_Human">
             <output>
                 <column name="id" />
--- a/tool_data_table_conf.xml.sample	Wed Jan 08 15:15:16 2020 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Jan 21 16:18:05 2020 +0000
@@ -12,6 +12,10 @@
     <columns>id, release, name, tissue, value</columns>
     <file path="tool-data/proteore_protein_atlas_tumor_tissue.loc" />
   </table>
+  <table name="proteore_protein_full_atlas" comment_char="#">
+    <columns>id, release, name, tissue, value</columns>
+    <file path="tool-data/proteore_protein_full_atlas.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" />