Mercurial > repos > proteore > proteore_data_manager
changeset 48:09d9fd9b2d8c draft
"planemo upload commit 714703437f238e7295980f96620365b801fd435c-dirty"
| author | proteore |
|---|---|
| date | Fri, 31 Jan 2020 15:51:40 +0000 |
| parents | f89ddc972ad4 |
| children | 1c40456be1db |
| files | data_manager/resource_building.py data_manager/resource_building.xml data_manager_conf.xml tool-data/proteore_protein_atlas_rna_tissue.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 5 files changed, 29 insertions(+), 1 deletions(-) [+] |
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--- a/data_manager/resource_building.py Tue Jan 21 16:26:56 2020 +0000 +++ b/data_manager/resource_building.py Fri Jan 31 15:51:40 2020 +0000 @@ -48,6 +48,10 @@ tissue_name = "HPA full atlas" url = "https://www.proteinatlas.org/download/proteinatlas.tsv.zip" table = "proteore_protein_full_atlas" + elif tissue == "HPA_RNA_tissue": + tissue_name = "HPA RNA tissue" + url = "https://www.proteinatlas.org/download/normal_tissue.tsv.zip" + table = "proteore_protein_atlas_rna_tissue" output_file = tissue +"_"+ time.strftime("%d-%m-%Y") + ".tsv" path = os.path.join(target_directory, output_file)
--- a/data_manager/resource_building.xml Tue Jan 21 16:26:56 2020 +0000 +++ b/data_manager/resource_building.xml Fri Jan 31 15:51:40 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.01.21.1" tool_type="manage_data"> +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.01.31" tool_type="manage_data"> <description> to create or update reference files for proteore tools </description> @@ -45,6 +45,7 @@ <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_RNA_tissue">RNA Tissue</option> </param> </when> <when value="peptide_atlas">
--- a/data_manager_conf.xml Tue Jan 21 16:26:56 2020 +0000 +++ b/data_manager_conf.xml Fri Jan 31 15:51:40 2020 +0000 @@ -31,6 +31,21 @@ </column> </output> </data_table> + <data_table name="proteore_protein_atlas_rna_tissue"> + <output> + <column name="id"/> + <column name="release"/> + <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/${release}.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"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_protein_atlas_rna_tissue.loc.sample Fri Jan 31 15:51:40 2020 +0000 @@ -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> <release> <name> <tissue> <value> +#9979819281 HPA_RNA_tissue_19-07-2018 HPA RNA tissue 19/07/2018 HPA_rna_tissue /projet/galaxydev/galaxy/tool-data/protein_atlas/projet/galaxydev/galaxy/database/jobs_directory/019/19159/dataset_39307_files/HPA_rna_tissue_19-07-2018.tsv
--- a/tool_data_table_conf.xml.sample Tue Jan 21 16:26:56 2020 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jan 31 15:51:40 2020 +0000 @@ -8,6 +8,10 @@ <columns>id, release, name, tissue, value</columns> <file path="tool-data/proteore_protein_atlas_normal_tissue.loc" /> </table> + <table name="proteore_protein_atlas_rna_tissue" comment_char="#"> + <columns>id, release, name, tissue, value</columns> + <file path="tool-data/proteore_protein_atlas_rna_tissue.loc" /> + </table> <table name="proteore_protein_atlas_tumor_tissue" comment_char="#"> <columns>id, release, name, tissue, value</columns> <file path="tool-data/proteore_protein_atlas_tumor_tissue.loc" />
