Mercurial > repos > dchristiany > data_manager_proteore
changeset 11:4bb219eee10f draft
planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty
| author | dchristiany |
|---|---|
| date | Tue, 23 Oct 2018 08:00:49 -0400 |
| parents | 2f153b41b6fe |
| children | 60cb0a5ae661 |
| files | data_manager/resource_building.xml tool-data/id_mapping.loc.sample tool-data/peptide_atlas.loc.sample tool-data/protein_atlas.loc.sample tool-data/proteore_id_mapping.loc.sample tool-data/proteore_peptide_atlas.loc.sample tool-data/proteore_protein_atlas.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 8 files changed, 28 insertions(+), 28 deletions(-) [+] |
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--- a/data_manager/resource_building.xml Tue Oct 23 07:43:37 2018 -0400 +++ b/data_manager/resource_building.xml Tue Oct 23 08:00:49 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2018.10.23" tool_type="manage_data"> +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2018.10.23.2" tool_type="manage_data"> <description> to create or update reference files for proteore tools </description>
--- a/tool-data/id_mapping.loc.sample Tue Oct 23 07:43:37 2018 -0400 +++ /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_file.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/peptide_atlas.loc.sample Tue Oct 23 07:43:37 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -#This file lists the locations name and values of reference files for number of MS/MS observations in a tissue -#This is a tab separated file (TAB, not 4 spaces !) -#<id> <name> <tissue> <value> -#Human_Heart_20-07-2018 Human Heart 20/07/2018 Human_Heart /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Heart_20-07-2018.tsv -#Human_Liver_20-07-2018 Human Liver 20/07/2018 Human_Liver /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Liver_20-07-2018.tsv -#Human_Urine_20-07-2018 Human Urine 20/07/2018 Human_Urine /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Urine_20-07-2018.tsv -#Human_Brain_20-07-2018 Human Brain 20/07/2018 Human_Brain /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Brain_20-07-2018.tsv -#Human_Kidney_20-07-2018 Human Kidney 20/07/2018 Human_Kidney /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Kidney_20-07-2018.tsv -#Human_Plasma_20-07-2018 Human Plasma 20/07/2018 Human_Plasma /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Plasma_20-07-2018.tsv -#Human_CSF_20-07-2018 Human CSF 20/07/2018 Human_CSF /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_CSF_20-07-2018.tsv
--- a/tool-data/protein_atlas.loc.sample Tue Oct 23 07:43:37 2018 -0400 +++ /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> <value> <path> -#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_id_mapping.loc.sample Tue Oct 23 08:00:49 2018 -0400 @@ -0,0 +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 +#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_peptide_atlas.loc.sample Tue Oct 23 08:00:49 2018 -0400 @@ -0,0 +1,10 @@ +#This file lists the locations name and values of reference files for number of MS/MS observations in a tissue +#This is a tab separated file (TAB, not 4 spaces !) +#<id> <name> <tissue> <value> +#Human_Heart_20-07-2018 Human Heart 20/07/2018 Human_Heart /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Heart_20-07-2018.tsv +#Human_Liver_20-07-2018 Human Liver 20/07/2018 Human_Liver /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Liver_20-07-2018.tsv +#Human_Urine_20-07-2018 Human Urine 20/07/2018 Human_Urine /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Urine_20-07-2018.tsv +#Human_Brain_20-07-2018 Human Brain 20/07/2018 Human_Brain /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Brain_20-07-2018.tsv +#Human_Kidney_20-07-2018 Human Kidney 20/07/2018 Human_Kidney /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Kidney_20-07-2018.tsv +#Human_Plasma_20-07-2018 Human Plasma 20/07/2018 Human_Plasma /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Plasma_20-07-2018.tsv +#Human_CSF_20-07-2018 Human CSF 20/07/2018 Human_CSF /projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_CSF_20-07-2018.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_protein_atlas.loc.sample Tue Oct 23 08:00:49 2018 -0400 @@ -0,0 +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> +#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 Tue Oct 23 07:43:37 2018 -0400 +++ b/tool_data_table_conf.xml.sample Tue Oct 23 08:00:49 2018 -0400 @@ -1,15 +1,15 @@ <?xml version="1.0"?> <tables> - <table name='peptide_atlas' comment_char="#"> + <table name='proteore_peptide_atlas' comment_char="#"> <columns>id, name, tissue, value</columns> - <file path="tool-data/peptide_atlas.loc"/> + <file path="tool-data/proteore_peptide_atlas.loc"/> </table> - <table name="protein_atlas" comment_char="#"> + <table name="proteore_protein_atlas" comment_char="#"> <columns>id, name, value, path</columns> - <file path="tool-data/protein_atlas.loc" /> + <file path="tool-data/proteore_protein_atlas.loc" /> </table> - <table name="id_mapping" comment_char="#"> + <table name="proteore_id_mapping" comment_char="#"> <columns>id, name, value, path</columns> - <file path="tool-data/id_mapping.loc" /> + <file path="tool-data/proteore_id_mapping.loc" /> </table> </tables>