Mercurial > repos > dchristiany > data_manager_proteore

changeset 6:9c75521e4a64 draft

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planemo upload commit d703392579d96e480c6461ce679516b12cefb3de-dirty
author dchristiany
date Fri, 19 Oct 2018 04:19:36 -0400
parents 1dc87bb457c7
children d16a52bf0e5b
files data_manager/resource_building.py data_manager/resource_building.xml data_manager_conf.xml tool_data_table_conf.xml.sample
diffstat 4 files changed, 4 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.py	Fri Oct 19 04:14:34 2018 -0400
+++ b/data_manager/resource_building.py	Fri Oct 19 04:19:36 2018 -0400
@@ -218,7 +218,7 @@
     name = name_dict[species]+" ("+time.strftime("%d-%m-%Y")+")"
 
     data_table_entry = dict(value = species+"_id_mapping_"+ time.strftime("%d-%m-%Y"), name = name, path = path)
-    _add_data_table_entry(data_manager_dict, data_table_entry, "id_mapping_tab")
+    _add_data_table_entry(data_manager_dict, data_table_entry, "id_mapping")
 
 def download_from_uniprot_ftp(file,target_directory) :
     ftp_dir = "pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/"
--- a/data_manager/resource_building.xml	Fri Oct 19 04:14:34 2018 -0400
+++ b/data_manager/resource_building.xml	Fri Oct 19 04:19:36 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="0.4" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="0.5" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
--- a/data_manager_conf.xml	Fri Oct 19 04:14:34 2018 -0400
+++ b/data_manager_conf.xml	Fri Oct 19 04:19:36 2018 -0400
@@ -28,7 +28,7 @@
                 </column>
             </output>
         </data_table>
-        <data_table name="id_mapping_tab">
+        <data_table name="id_mapping">
             <output>
                 <column name="value" />
                 <column name="name" />
--- a/tool_data_table_conf.xml.sample	Fri Oct 19 04:14:34 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Fri Oct 19 04:19:36 2018 -0400
@@ -4,11 +4,7 @@
         <columns>tissue,name,value</columns>
         <file path="tool-data/peptide_atlas.loc"/>
     </table>
-    <table name="proteinatlas" comment_char="#">
-      <columns>name, value, path</columns>
-      <file path="tool-data/proteinatlas.loc" />
-    </table>
-    <table name="id_mapping_tab" comment_char="#">
+    <table name="id_mapping" comment_char="#">
       <columns>name, value, path</columns>
       <file path="tool-data/id_mapping.loc" />
     </table>