Mercurial > repos > proteore > proteore_data_manager

changeset 3:18d3b1ea7a18 draft

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planemo upload commit c6e1fd1f68e81ce9eea6ad66adee21070f2893ef-dirty
author proteore
date Wed, 06 Mar 2019 09:50:27 -0500
parents 2e34ee6d2d37
children ce01295cd601
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, 11 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.py	Wed Mar 06 08:57:43 2019 -0500
+++ b/data_manager/resource_building.py	Wed Mar 06 09:50:27 2019 -0500
@@ -231,7 +231,7 @@
     name = species +" (" + name_dict[species]+" "+time.strftime("%d/%m/%Y")+")"
     id = species+"_id_mapping_"+ time.strftime("%d-%m-%Y")
 
-    data_table_entry = dict(id=id, name = name, value = species, path = path)
+    data_table_entry = dict(id=id, 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) :
--- a/data_manager/resource_building.xml	Wed Mar 06 08:57:43 2019 -0500
+++ b/data_manager/resource_building.xml	Wed Mar 06 09:50:27 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.06.1" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.06.2" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
--- a/data_manager_conf.xml	Wed Mar 06 08:57:43 2019 -0500
+++ b/data_manager_conf.xml	Wed Mar 06 09:50:27 2019 -0500
@@ -48,8 +48,8 @@
             <output>
                 <column name="id" />
                 <column name="name" />
-                <column name="value" />
-                <column name="path" output_ref="output" >
+                <column name="species" />
+                <column name="value" output_ref="output" >
                     <move type="file">
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
@@ -63,8 +63,8 @@
             <output>
                 <column name="id" />
                 <column name="name" />
-                <column name="value" />
-                <column name="path" output_ref="output" >
+                <column name="species" />
+                <column name="value" output_ref="output" >
                     <move type="file">
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
@@ -78,8 +78,8 @@
             <output>
                 <column name="id" />
                 <column name="name" />
-                <column name="value" />
-                <column name="path" output_ref="output" >
+                <column name="species" />
+                <column name="value" output_ref="output" >
                     <move type="file">
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
--- a/tool_data_table_conf.xml.sample	Wed Mar 06 08:57:43 2019 -0500
+++ b/tool_data_table_conf.xml.sample	Wed Mar 06 09:50:27 2019 -0500
@@ -13,15 +13,15 @@
       <file path="tool-data/proteore_protein_atlas_tumor_tissue.loc" />
     </table>
     <table name="proteore_id_mapping_Human" comment_char="#">
-      <columns>id, name, value, path</columns>
+      <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, value, path</columns>
+      <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, value, path</columns>
+      <columns>id, name, species, value</columns>
       <file path="tool-data/proteore_id_mapping_Rat.loc" />
     </table>
     <table name="proteore_biogrid_dictionaries" comment_char="#">