Mercurial > repos > dchristiany > data_manager_proteore
changeset 12:60cb0a5ae661 draft
planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
| author | dchristiany |
|---|---|
| date | Tue, 23 Oct 2018 08:18:32 -0400 |
| parents | 4bb219eee10f |
| children | a1530507fee4 |
| files | data_manager/resource_building.py data_manager/resource_building.xml data_manager_conf.xml |
| diffstat | 3 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager/resource_building.py Tue Oct 23 08:00:49 2018 -0400 +++ b/data_manager/resource_building.py Tue Oct 23 08:18:32 2018 -0400 @@ -52,7 +52,7 @@ tissue_id = tissue_name.replace(" ","_").replace("/","-") data_table_entry = dict(id=tissue_id, name = tissue_name, value = tissue, path = path) - _add_data_table_entry(data_manager_dict, data_table_entry, "protein_atlas") + _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_protein_atlas") ####################################################################################################### @@ -90,7 +90,7 @@ w.writerows(uni_dict.items()) data_table_entry = dict(id=tissue_id, name=tissue_name, value = path, tissue = tissue) - _add_data_table_entry(data_manager_dict, data_table_entry, "peptide_atlas") + _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_peptide_atlas") #function to count the number of observations by uniprot id def build_dictionary (csv) : @@ -221,7 +221,7 @@ id = species+"_id_mapping_"+ time.strftime("%d-%m-%Y") data_table_entry = dict(id=id, name = name, value = species, path = path) - _add_data_table_entry(data_manager_dict, data_table_entry, "id_mapping") + _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_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 Tue Oct 23 08:00:49 2018 -0400 +++ b/data_manager/resource_building.xml Tue Oct 23 08:18:32 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2018.10.23.2" tool_type="manage_data"> +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2018.10.23.3" tool_type="manage_data"> <description> to create or update reference files for proteore tools </description>
--- a/data_manager_conf.xml Tue Oct 23 08:00:49 2018 -0400 +++ b/data_manager_conf.xml Tue Oct 23 08:18:32 2018 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <data_managers> <data_manager tool_file="data_manager/resource_building.xml" id="resource_building"> - <data_table name="protein_atlas"> + <data_table name="proteore_protein_atlas"> <output> <column name="id"/> <column name="name" /> @@ -15,7 +15,7 @@ </column> </output> </data_table> - <data_table name="peptide_atlas"> + <data_table name="proteore_peptide_atlas"> <output> <column name="id"/> <column name="name" /> @@ -30,7 +30,7 @@ </column> </output> </data_table> - <data_table name="id_mapping"> + <data_table name="proteore_id_mapping"> <output> <column name="id" /> <column name="name" />