Mercurial > repos > dchristiany > data_manager_proteore

changeset 51:8f6ddad93e9f draft

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planemo upload commit 12b0b3e18cd7af9a8588906fa2ec199b9d2a770f-dirty
author dchristiany
date Fri, 01 Mar 2019 09:37:07 -0500
parents 932950befe87
children a34897a85cda
files data_manager/resource_building.py data_manager/resource_building.xml data_manager_conf.xml tool-data/proteore_biogrid_dictionaries.loc.sample tool-data/proteore_bioplex_dictionaries.loc.sample tool-data/proteore_humap_dictionaries.loc.sample tool-data/proteore_id_mapping.loc.sample tool-data/proteore_protein_atlas.loc.sample tool_data_table_conf.xml.sample
diffstat 9 files changed, 22 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.py	Fri Feb 01 11:22:06 2019 -0500
+++ b/data_manager/resource_building.py	Fri Mar 01 09:37:07 2019 -0500
@@ -52,7 +52,7 @@
     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, value = tissue, path = path)
+    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")
 
 
@@ -476,7 +476,7 @@
     with open(path, 'w') as handle:
         json.dump(dico, handle, sort_keys=True)
 
-    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_"+interactome+"_dictionaries")
 
 
--- a/data_manager/resource_building.xml	Fri Feb 01 11:22:06 2019 -0500
+++ b/data_manager/resource_building.xml	Fri Mar 01 09:37:07 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.02.01.4" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.01" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
--- a/data_manager_conf.xml	Fri Feb 01 11:22:06 2019 -0500
+++ b/data_manager_conf.xml	Fri Mar 01 09:37:07 2019 -0500
@@ -5,8 +5,8 @@
             <output>
                 <column name="id"/>
                 <column name="name" />
-                <column name="value" />
-                <column name="path" output_ref="output" >
+                <column name="tissue" />
+                <column name="value" output_ref="output" >
                     <move type="file">
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
                     </move>
@@ -49,8 +49,8 @@
             <output>
                 <column name="id" />
                 <column name="name" />
-                <column name="value" />
-                <column name="path" output_ref="output" >
+                <column name="species" />
+                <column name="value" output_ref="output" >
                     <move type="file">
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
@@ -64,8 +64,8 @@
             <output>
                 <column name="id" />
                 <column name="name" />
-                <column name="value" />
-                <column name="path" output_ref="output" >
+                <column name="species" />
+                <column name="value" output_ref="output" >
                     <move type="file">
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
@@ -79,8 +79,8 @@
             <output>
                 <column name="id" />
                 <column name="name" />
-                <column name="value" />
-                <column name="path" output_ref="output" >
+                <column name="species" />
+                <column name="value" output_ref="output" >
                     <move type="file">
                         <!--source>${path}</source-->
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
--- a/tool-data/proteore_biogrid_dictionaries.loc.sample	Fri Feb 01 11:22:06 2019 -0500
+++ b/tool-data/proteore_biogrid_dictionaries.loc.sample	Fri Mar 01 09:37:07 2019 -0500
@@ -1,4 +1,4 @@
-#id	name	value	path
-#biogrid_human_08-01-2019	Human (Homo sapiens)	Human	PPI_dictionaries/Human_biogrid.json
-#biogrid_mouse_08-01-2019	Mouse (Mus musculus)	Mouse	PPI_dictionaries/Mouse_biogrid.json
-#biogrid_rat_08-01-2019	Rat (Rattus norvegicus) Rat	PPI_dictionaries/Rat_biogrid.json
+#id	name	species	value
+#biogrid_human_08-01-2019	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/Human_biogrid.json
+#biogrid_mouse_08-01-2019	Mouse (Mus musculus) 08/01/2019	Mouse	PPI_dictionaries/Mouse_biogrid.json
+#biogrid_rat_08-01-2019	Rat (Rattus norvegicus) 08/01/2019 Rat	PPI_dictionaries/Rat_biogrid.json
--- a/tool-data/proteore_bioplex_dictionaries.loc.sample	Fri Feb 01 11:22:06 2019 -0500
+++ b/tool-data/proteore_bioplex_dictionaries.loc.sample	Fri Mar 01 09:37:07 2019 -0500
@@ -1,4 +1,2 @@
-#id	name	value	path
-#bioplex_human_08-01-2019	Human (Homo sapiens)	Human	PPI_dictionaries/human_bioplex.json
-#bioplex_mouse_08-01-2019	Mouse (Mus musculus)	Mouse	PPI_dictionaries/mouse_bioplex.json
-#bioplex_rat_08-01-2019	Rat (Rattus norvegicus)	Rat	PPI_dictionaries/rat_bioplexdico.json
+#id	name	species	value
+#bioplex_human_08-01-2019	Human (Homo sapiens) 08/01/2019	Human	PPI_dictionaries/human_bioplex.json
--- a/tool-data/proteore_humap_dictionaries.loc.sample	Fri Feb 01 11:22:06 2019 -0500
+++ b/tool-data/proteore_humap_dictionaries.loc.sample	Fri Mar 01 09:37:07 2019 -0500
@@ -1,2 +1,2 @@
-#id	name	value	path
-#humap_human_01-02-2019	Human (Homo sapiens) 01/02/19	Human	PPI_dictionaries/Human_humap_01-02-2019.json
+#id	name	species	value
+#humap_human_01-02-2019 Human (Homo sapiens) 01/02/19	Human	PPI_dictionaries/Human_humap_01-02-2019.json
--- a/tool-data/proteore_id_mapping.loc.sample	Fri Feb 01 11:22:06 2019 -0500
+++ b/tool-data/proteore_id_mapping.loc.sample	Fri Mar 01 09:37:07 2019 -0500
@@ -1,5 +1,5 @@
 #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_file.tsv
+#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
--- a/tool-data/proteore_protein_atlas.loc.sample	Fri Feb 01 11:22:06 2019 -0500
+++ b/tool-data/proteore_protein_atlas.loc.sample	Fri Mar 01 09:37:07 2019 -0500
@@ -1,6 +1,6 @@
 #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> <value>	<path>
+#<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
--- a/tool_data_table_conf.xml.sample	Fri Feb 01 11:22:06 2019 -0500
+++ b/tool_data_table_conf.xml.sample	Fri Mar 01 09:37:07 2019 -0500
@@ -5,7 +5,7 @@
       <file path="tool-data/proteore_peptide_atlas.loc"/>
     </table>
     <table name="proteore_protein_atlas" comment_char="#">
-      <columns>id, name, value, path</columns>
+      <columns>id, name, tissue, value</columns>
       <file path="tool-data/proteore_protein_atlas.loc" />
     </table>
     <table name="proteore_id_mapping" comment_char="#">