Mercurial > repos > proteore > proteore_data_manager
changeset 1:0915249b8c4b draft
planemo upload commit 4dd1a2f7d196a1d2e70fab379a2c08367da0fe94-dirty
| author | proteore |
|---|---|
| date | Wed, 06 Mar 2019 08:53:06 -0500 |
| parents | 0a26460d7366 |
| children | 2e34ee6d2d37 |
| files | data_manager/resource_building.py data_manager/resource_building.xml data_manager_conf.xml tool-data/proteore_id_mapping.loc.sample tool-data/proteore_id_mapping_Human.loc.sample tool-data/proteore_id_mapping_Mouse.loc.sample tool-data/proteore_id_mapping_Rat.loc.sample tool-data/proteore_protein_atlas.loc.sample tool-data/proteore_protein_atlas_normal_tissue.loc.sample tool-data/proteore_protein_atlas_tumor_tissue.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 11 files changed, 88 insertions(+), 21 deletions(-) [+] |
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--- a/data_manager/resource_building.py Mon Mar 04 05:03:04 2019 -0500 +++ b/data_manager/resource_building.py Wed Mar 06 08:53:06 2019 -0500 @@ -39,12 +39,15 @@ if tissue == "HPA_normal_tissue": tissue_name = "HPA normal tissue" url = "https://www.proteinatlas.org/download/normal_tissue.tsv.zip" + table = "proteore_protein_atlas_normal_tissue" elif tissue == "HPA_pathology": tissue_name = "HPA pathology" url = "https://www.proteinatlas.org/download/pathology.tsv.zip" + table = "proteore_protein_atlas_tumor_tissue" elif tissue == "HPA_full_atlas": tissue_name = "HPA full atlas" url = "https://www.proteinatlas.org/download/proteinatlas.tsv.zip" + table = "proteore_protein_full_atlas" output_file = tissue +"_"+ time.strftime("%d-%m-%Y") + ".tsv" path = os.path.join(target_directory, output_file) @@ -52,8 +55,9 @@ 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, tissue = tissue, value = path) - _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_protein_atlas") + _add_data_table_entry(data_manager_dict, data_table_entry, table) ####################################################################################################### @@ -228,7 +232,7 @@ 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, "proteore_id_mapping") + _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_idmapping_"+species) 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 Mon Mar 04 05:03:04 2019 -0500 +++ b/data_manager/resource_building.xml Wed Mar 06 08:53:06 2019 -0500 @@ -1,8 +1,9 @@ -<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.04" tool_type="manage_data"> +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.06" tool_type="manage_data"> <description> to create or update reference files for proteore tools </description> <requirements> + <!--requirement type="package" version="1.8.2">sparqlwrapper</requirement--> </requirements> <stdio> <exit_code range="1:" /> @@ -39,7 +40,7 @@ <param name="tissues" type="select" multiple="false" label="Please select tissue"> <option value="HPA_normal_tissue">Normal tissue</option> <option value="HPA_pathology">Pathology</option> - <option value="HPA_full_atlas">Full Atlas</option> + <!--option value="HPA_full_atlas">Full Atlas</option--> </param> </when> <when value="peptide_atlas">
--- a/data_manager_conf.xml Mon Mar 04 05:03:04 2019 -0500 +++ b/data_manager_conf.xml Wed Mar 06 08:53:06 2019 -0500 @@ -1,7 +1,21 @@ <?xml version="1.0"?> <data_managers> <data_manager tool_file="data_manager/resource_building.xml" id="resource_building"> - <data_table name="proteore_protein_atlas"> + <data_table name="proteore_protein_atlas_normal_tissue"> + <output> + <column name="id"/> + <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/${id}.tsv</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="proteore_protein_atlas_tumor_tissue"> <output> <column name="id"/> <column name="name" /> @@ -30,7 +44,37 @@ </column> </output> </data_table> - <data_table name="proteore_id_mapping"> + <data_table name="proteore_id_mapping_Human"> + <output> + <column name="id" /> + <column name="name" /> + <column name="value" /> + <column name="path" output_ref="output" > + <move type="file"> + <!--source>${path}</source--> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="proteore_id_mapping_Mouse"> + <output> + <column name="id" /> + <column name="name" /> + <column name="value" /> + <column name="path" output_ref="output" > + <move type="file"> + <!--source>${path}</source--> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${id}.tsv</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="proteore_id_mapping_Rat"> <output> <column name="id" /> <column name="name" />
--- a/tool-data/proteore_id_mapping.loc.sample Mon Mar 04 05:03:04 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#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.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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_id_mapping_Human.loc.sample Wed Mar 06 08:53:06 2019 -0500 @@ -0,0 +1,3 @@ +#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.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_id_mapping_Mouse.loc.sample Wed Mar 06 08:53:06 2019 -0500 @@ -0,0 +1,3 @@ +#This file lists the locations of reference file for id_converter tool +#<id> <name> <value> <path> +#mouse_id_mapping_01-01-2018 Mouse (Mus musculus) mouse_id_mapping tool-data/mouse_id_mapping.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_id_mapping_Rat.loc.sample Wed Mar 06 08:53:06 2019 -0500 @@ -0,0 +1,3 @@ +#This file lists the locations of reference file for id_converter tool +#<id> <name> <value> <path> +#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 Mon Mar 04 05:03:04 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -#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> <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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_protein_atlas_normal_tissue.loc.sample Wed Mar 06 08:53:06 2019 -0500 @@ -0,0 +1,4 @@ +#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> <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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_protein_atlas_tumor_tissue.loc.sample Wed Mar 06 08:53:06 2019 -0500 @@ -0,0 +1,4 @@ +#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> <tissue> <value> +#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
--- a/tool_data_table_conf.xml.sample Mon Mar 04 05:03:04 2019 -0500 +++ b/tool_data_table_conf.xml.sample Wed Mar 06 08:53:06 2019 -0500 @@ -4,13 +4,25 @@ <columns>id, name, tissue, value</columns> <file path="tool-data/proteore_peptide_atlas.loc"/> </table> - <table name="proteore_protein_atlas" comment_char="#"> + <table name="proteore_protein_atlas_normal_tissue" comment_char="#"> <columns>id, name, tissue, value</columns> - <file path="tool-data/proteore_protein_atlas.loc" /> + <file path="tool-data/proteore_protein_atlas_normal_tissue.loc" /> + </table> + <table name="proteore_protein_atlas_tumor_tissue" comment_char="#"> + <columns>id, name, tissue, value</columns> + <file path="tool-data/proteore_protein_atlas_tumor_tissue.loc" /> </table> - <table name="proteore_id_mapping" comment_char="#"> + <table name="proteore_id_mapping_Human" comment_char="#"> + <columns>id, name, value, path</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> - <file path="tool-data/proteore_id_mapping.loc" /> + <file path="tool-data/proteore_id_mapping_Mouse.loc" /> + </table> + <table name="proteore_id_mapping_Rat" comment_char="#"> + <columns>id, name, value, path</columns> + <file path="tool-data/proteore_id_mapping_Rat.loc" /> </table> <table name="proteore_biogrid_dictionaries" comment_char="#"> <columns>id, name, species, value</columns>