| Previous changeset 4:e967a99d66b3 (2020-01-23) Next changeset 6:8f33a6e6e36c (2020-06-10) |
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Commit message:
"planemo upload commit a23ff40d482d58e0425108bf60372e5fcafb847e" |
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modified:
data_manager/resource_building.py data_manager/resource_building.xml data_manager_conf.xml tool_data_table_conf.xml.sample |
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added:
tool-data/proteore_protein_atlas_rna_tissue.loc.sample |
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| diff -r e967a99d66b3 -r b05fa99ddda2 data_manager/resource_building.py --- a/data_manager/resource_building.py Thu Jan 23 08:38:02 2020 -0500 +++ b/data_manager/resource_building.py Thu Feb 06 04:02:50 2020 -0500 |
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| @@ -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/rna_tissue_consensus.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) |
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| diff -r e967a99d66b3 -r b05fa99ddda2 data_manager/resource_building.xml --- a/data_manager/resource_building.xml Thu Jan 23 08:38:02 2020 -0500 +++ b/data_manager/resource_building.xml Thu Feb 06 04:02:50 2020 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.01.21" tool_type="manage_data"> +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.02.06" 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"> |
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| diff -r e967a99d66b3 -r b05fa99ddda2 data_manager_conf.xml --- a/data_manager_conf.xml Thu Jan 23 08:38:02 2020 -0500 +++ b/data_manager_conf.xml Thu Feb 06 04:02:50 2020 -0500 |
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| @@ -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"/> |
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| diff -r e967a99d66b3 -r b05fa99ddda2 tool-data/proteore_protein_atlas_rna_tissue.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_protein_atlas_rna_tissue.loc.sample Thu Feb 06 04:02:50 2020 -0500 |
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| @@ -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 |
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| diff -r e967a99d66b3 -r b05fa99ddda2 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Jan 23 08:38:02 2020 -0500 +++ b/tool_data_table_conf.xml.sample Thu Feb 06 04:02:50 2020 -0500 |
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| @@ -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" /> |