| Next changeset 1:f3507260b30f (2019-04-16) |
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Commit message:
planemo upload commit 567ba7934c0ca55529dfeb5e7ca0935ace260ad7-dirty |
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added:
data_manager/resource_building.py data_manager/resource_building.xml data_manager_conf.xml tool-data/proteore_biogrid_dictionaries.loc.sample tool-data/proteore_bioplex_dictionaries.loc.sample tool-data/proteore_humap_dictionaries.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_nextprot_ref.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 |
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| diff -r 000000000000 -r 9e31ea9fc7ea data_manager/resource_building.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/resource_building.py Wed Mar 13 06:30:42 2019 -0400 |
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| b'@@ -0,0 +1,649 @@\n+# -*- coding: utf-8 -*-\n+"""\n+The purpose of this script is to create source files from different databases to be used in other proteore tools\n+"""\n+\n+import os, sys, argparse, requests, time, csv, re, json, shutil, zipfile\n+from io import BytesIO\n+from zipfile import ZipFile\n+from galaxy.util.json import from_json_string, to_json_string\n+\n+#######################################################################################################\n+# General functions\n+#######################################################################################################\n+def unzip(url, output_file):\n+ """\n+ Get a zip file content from a link and unzip\n+ """\n+ content = requests.get(url)\n+ zipfile = ZipFile(BytesIO(content.content))\n+ output_content = ""\n+ output_content += zipfile.open(zipfile.namelist()[0]).read()\n+ output = open(output_file, "w")\n+ output.write(output_content)\n+ output.close()\n+\n+def _add_data_table_entry(data_manager_dict, data_table_entry,data_table):\n+ data_manager_dict[\'data_tables\'] = data_manager_dict.get(\'data_tables\', {})\n+ data_manager_dict[\'data_tables\'][data_table] = data_manager_dict[\'data_tables\'].get(data_table, [])\n+ data_manager_dict[\'data_tables\'][data_table].append(data_table_entry)\n+ return data_manager_dict\n+\n+#######################################################################################################\n+# 1. Human Protein Atlas\n+# - Normal tissue\n+# - Pathology\n+# - Full Atlas\n+#######################################################################################################\n+def HPA_sources(data_manager_dict, tissue, target_directory):\n+ if tissue == "HPA_normal_tissue":\n+ tissue_name = "HPA normal tissue"\n+ url = "https://www.proteinatlas.org/download/normal_tissue.tsv.zip"\n+ table = "proteore_protein_atlas_normal_tissue"\n+ elif tissue == "HPA_pathology":\n+ tissue_name = "HPA pathology"\n+ url = "https://www.proteinatlas.org/download/pathology.tsv.zip"\n+ table = "proteore_protein_atlas_tumor_tissue"\n+ elif tissue == "HPA_full_atlas":\n+ tissue_name = "HPA full atlas"\n+ url = "https://www.proteinatlas.org/download/proteinatlas.tsv.zip"\n+ table = "proteore_protein_full_atlas"\n+ \n+ output_file = tissue +"_"+ time.strftime("%d-%m-%Y") + ".tsv"\n+ path = os.path.join(target_directory, output_file)\n+ unzip(url, path) #download and save file\n+ tissue_name = tissue_name + " " + time.strftime("%d/%m/%Y")\n+ tissue_id = tissue_name.replace(" ","_").replace("/","-")\n+\n+\n+ data_table_entry = dict(id=tissue_id, name = tissue_name, tissue = tissue, value = path)\n+ _add_data_table_entry(data_manager_dict, data_table_entry, table)\n+\n+\n+#######################################################################################################\n+# 2. Peptide Atlas\n+#######################################################################################################\n+def peptide_atlas_sources(data_manager_dict, tissue, date, target_directory):\n+ # Define organism_id (here Human) - to be upraded when other organism added to the project\n+ organism_id = "2"\n+ # Extract sample_category_id and output filename\n+ tissue=tissue.split(".")\n+ sample_category_id = tissue[0]\n+ tissue_name = tissue[1]\n+ output_file = tissue_name+"_"+date + ".tsv"\n+\n+ query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+ \\\n+ sample_category_id+"&display_options=ShowAbundances&organism_id="+organism_id+ \\\n+ "&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf\\\n+ &QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY"\n+\n+ with requests.Session() as s:\n+ download = s.get(query)\n+ decoded_content = download.content.decode(\'utf-8\')\n+ cr = csv.reader(decoded_content.splitlines(), delimiter=\'\\t\')\n+\n+ uni_dict = bu'..b' = tm_domains["properties"]\n+ for domain in domains :\n+ if domain["name"]=="region structure" and domain["value"]=="Helical" :\n+ nb_domains+=1\n+\n+ \n+ nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence])\n+ \n+ output_file = \'nextprot_ref_\'+ time.strftime("%d-%m-%Y") + ".tsv"\n+ path = os.path.join(target_directory,output_file)\n+ name = "neXtProt release "+time.strftime("%d-%m-%Y")\n+ id = "nextprot_ref_"+time.strftime("%d-%m-%Y")\n+\n+ with open(path, \'w\') as output:\n+ writer = csv.writer(output,delimiter="\\t")\n+ writer.writerows(nextprot_file)\n+\n+ data_table_entry = dict(id=id, name = name, value = path)\n+ _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_nextprot_ref")\n+\n+#######################################################################################################\n+# Main function\n+#######################################################################################################\n+def main():\n+ parser = argparse.ArgumentParser()\n+ parser.add_argument("--hpa", metavar = ("HPA_OPTION"))\n+ parser.add_argument("--peptideatlas", metavar=("SAMPLE_CATEGORY_ID"))\n+ parser.add_argument("--id_mapping", metavar = ("ID_MAPPING_SPECIES"))\n+ parser.add_argument("--interactome", metavar = ("PPI"))\n+ parser.add_argument("--species")\n+ parser.add_argument("--date")\n+ parser.add_argument("-o", "--output")\n+ parser.add_argument("--database")\n+ args = parser.parse_args()\n+\n+ data_manager_dict = {}\n+ # Extract json file params\n+ filename = args.output\n+ params = from_json_string(open(filename).read())\n+ target_directory = params[ \'output_data\' ][0][\'extra_files_path\']\n+ os.mkdir(target_directory)\n+\n+ ## Download source files from HPA\n+ try:\n+ hpa = args.hpa\n+ except NameError:\n+ hpa = None\n+ if hpa is not None:\n+ #target_directory = "/projet/galaxydev/galaxy/tools/proteore/ProteoRE/tools/resources_building/test-data/"\n+ hpa = hpa.split(",")\n+ for hpa_tissue in hpa:\n+ HPA_sources(data_manager_dict, hpa_tissue, target_directory)\n+ \n+ ## Download source file from Peptide Atlas query\n+ try:\n+ peptide_atlas = args.peptideatlas\n+ date = args.date\n+ except NameError:\n+ peptide_atlas = None\n+ if peptide_atlas is not None:\n+ #target_directory = "/projet/galaxydev/galaxy/tools/proteore/ProteoRE/tools/resources_building/test-data/"\n+ peptide_atlas = peptide_atlas.split(",")\n+ for pa_tissue in peptide_atlas:\n+ peptide_atlas_sources(data_manager_dict, pa_tissue, date, target_directory)\n+\n+ ## Download ID_mapping source file from Uniprot\n+ try:\n+ id_mapping=args.id_mapping\n+ except NameError:\n+ id_mapping = None\n+ if id_mapping is not None:\n+ id_mapping = id_mapping .split(",")\n+ for species in id_mapping :\n+ id_mapping_sources(data_manager_dict, species, target_directory)\n+\n+ ## Download PPI ref files from biogrid/bioplex/humap\n+ try:\n+ interactome=args.interactome\n+ if interactome == "biogrid" :\n+ species=args.species\n+ else :\n+ species="Human"\n+ except NameError:\n+ interactome=None\n+ species=None\n+ if interactome is not None and species is not None:\n+ PPI_ref_files(data_manager_dict, species, interactome, target_directory)\n+\n+ ## Build nextprot ref file for add protein features\n+ try:\n+ database=args.database\n+ except NameError:\n+ database=None\n+ if database is not None :\n+ Build_nextprot_ref_file(data_manager_dict,target_directory)\n+\n+ #save info to json file\n+ filename = args.output\n+ open(filename, \'wb\').write(to_json_string(data_manager_dict))\n+\n+if __name__ == "__main__":\n+ main()\n' |
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| diff -r 000000000000 -r 9e31ea9fc7ea data_manager/resource_building.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/resource_building.xml Wed Mar 13 06:30:42 2019 -0400 |
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| b'@@ -0,0 +1,223 @@\n+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.13" tool_type="manage_data">\n+<description>\n+to create or update reference files for proteore tools\n+</description>\n+<requirements>\n+ <!--requirement type="package" version="1.8.2">sparqlwrapper</requirement-->\n+</requirements>\n+<stdio>\n+ <exit_code range="1:" />\n+</stdio>\n+<command><![CDATA[\n+\n+ python $__tool_directory__/resource_building.py\n+ #if $database.database == "human_protein_atlas"\n+ --hpa "$database.tissues"\n+ #else if $database.database == "peptide_atlas"\n+ --peptideatlas="$database.tissues"\n+ --date="$database.date"\n+ #else if $database.database == "id_mapping"\n+ --id_mapping="$database.species"\n+ #else if $database.database == "PPI"\n+ --interactome="$database.base.interactome"\n+ #if $database.base.interactome == "biogrid"\n+ --species="$database.base.species"\n+ #end if\n+ #else if $database.database == "nextprot"\n+ --database=$database.database\n+ #end if\n+ --output "$output"\n+ \n+]]></command>\n+\n+<inputs>\n+ <conditional name="database">\n+ <param name="database" type="select">\n+ <option value="human_protein_atlas">Human Protein Atlas</option>\n+ <option value="peptide_atlas">Peptide Atlas</option>\n+ <option value="id_mapping">ID mapping</option>\n+ <option value="PPI">Build protein interaction maps</option>\n+ <option value="nextprot">neXtProt</option>\n+ </param>\n+ <when value="human_protein_atlas">\n+ <param name="tissues" type="select" multiple="false" label="Please select tissue">\n+ <option value="HPA_normal_tissue">Normal tissue</option>\n+ <option value="HPA_pathology">Pathology</option>\n+ <!--option value="HPA_full_atlas">Full Atlas</option-->\n+ </param>\n+ </when>\n+ <when value="peptide_atlas">\n+ <param name="tissues" type="select" multiple="false" label="Please select the tissue">\n+ <option value="432.Human_Adrenal_gland">Human Adrenal gland proteome</option>\n+ <option value="441.Human_Brain">Human Brain proteome</option>\n+ <option value="427.Human_Breast">Human Breast proteome</option>\n+ <option value="434.Human_CSF">Human CSF (Cerebro Spinal Fluid) proteome</option>\n+ <option value="374.Human_Colon_cancer">Human Colon cancer proteome</option>\n+ <option value="429.Human_Digestive_system">Human Digestive system proteome</option>\n+ <option value="430.Human_Female_reproductive_system">Human Female reproductive system proteome</option>\n+ <option value="418.Human_Heart">Human Heart proteome</option>\n+ <option value="424.Human_Kidney">Human Kidney proteome</option>\n+ <option value="425.Human_Liver">Human Liver proteome</option>\n+ <option value="419.Human_Lung">Human Lung proteome</option>\n+ <option value="431.Human_Male_reproductive_system">Human Male reproductive system proteome</option>\n+ <option value="420.Human_Pancreas">Human Pancreas proteome</option>\n+ <option value="465.Human_Plasma_non_glyco">Human Plasma non glyco proteome</option>\n+ <option value="421.Human_Spleen">Human Spleen proteome</option>\n+ <option value="463.Human_Testis">Human Testis proteome</option>\n+ <option value="422.Human_Urinary_bladder">Human Bladder proteome</option>\n+ <option value="423.Human_Urine">Human Urine proteome</option>\n+ </param>\n+ <param name="date" type="text" value="" label="enter the build date" help="for example: \'2018-04\'"/>\n+ </when>\n+ <when value="id_mapping">\n+ <param name="species" type="select" multiple="false" label="Please select t'..b'e_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.\n+* `Human Plasma Non-Glyco proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=465&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.\n+* `Human Spleen proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=421&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.\n+* `Human Testis proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=463&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.\n+* `Human Urinary Bladder proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=422&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.\n+* `Human Urine proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=423&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY>`_.\n+\n+For ID mapping:\n+\n+* `HUMAN_9606_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz>`_.\n+* `HUMAN_9606_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz>`_.\n+* `nextprot_ac_list_all.txt <ftp://ftp.nextprot.org/pub/current_release/ac_lists/nextprot_ac_list_all.txt>`_.\n+* `MOUSE_10090_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping_selected.tab.gz>`_.\n+* `MOUSE_10090_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping.dat.gz>`_.\n+* `RAT_10116_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/RAT_10116_idmapping_selected.tab.gz>`_.\n+* `RAT_10116_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/RAT_10116_idmapping.dat.gz>`_.\n+\n+For Build protein interaction maps:\n+\n+* `BIOGRID_oragism <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.167/BIOGRID-ORGANISM-3.5.167.tab2.zip>`_.\n+* `NCBI2Reactome.txt <https://www.reactome.org/download/current/NCBI2Reactome.txt>`_.\n+* `Bioplex_interactionList_v4a.tsv <http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv>`_.\n+* `UniProt2Reactome.txt <https://reactome.org/download/current/UniProt2Reactome.txt>`_.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Authors**\n+\n+David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR\n+\n+Sandra D\xc3\xa9rozier, Olivier Ru\xc3\xa9, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform\n+\n+This work has been partially funded through the French National Agency for Research (ANR) IFB project.\n+\n+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.\n+ \n+ ]]></help>\n+ <citations>\n+ </citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 9e31ea9fc7ea data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Wed Mar 13 06:30:42 2019 -0400 |
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| @@ -0,0 +1,152 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/resource_building.xml" id="resource_building"> + <data_table name="proteore_peptide_atlas"> + <output> + <column name="id"/> + <column name="name" /> + <column name="tissue" /> + <column name="value" output_ref="output" > + <move type="file"> + <!--source>${path}/${value}.tsv</source--> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">peptide_atlas/</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/peptide_atlas/${id}.tsv</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <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/${id}.tsv</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="proteore_protein_atlas_tumor_tissue"> + <output> + <column name="id"/> + <column name="name" /> + <column name="tissue" /> + <column name="value" output_ref="output" > + <move type="file"> + <target base="${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_id_mapping_Human"> + <output> + <column name="id" /> + <column name="name" /> + <column name="species" /> + <column name="value" 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="species" /> + <column name="value" 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" /> + <column name="species" /> + <column name="value" 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_biogrid_dictionaries"> + <output> + <column name="id" /> + <column name="name" /> + <column name="species" /> + <column name="value" output_ref="output" > + <move type="file"> + <!--source>${path}</source--> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="proteore_bioplex_dictionaries"> + <output> + <column name="id" /> + <column name="name" /> + <column name="species" /> + <column name="value" output_ref="output" > + <move type="file"> + <!--source>${path}</source--> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="proteore_humap_dictionaries"> + <output> + <column name="id" /> + <column name="name" /> + <column name="species" /> + <column name="value" output_ref="output" > + <move type="file"> + <!--source>${path}</source--> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${id}.json</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="proteore_nextprot_ref"> + <output> + <column name="id" /> + <column name="name" /> + <column name="value" output_ref="output" > + <move type="file"> + <!--source>${path}</source--> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">proteore_nextprot_ref/</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/proteore_nextprot_ref/${id}.tsv</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> |
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| diff -r 000000000000 -r 9e31ea9fc7ea tool-data/proteore_biogrid_dictionaries.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_biogrid_dictionaries.loc.sample Wed Mar 13 06:30:42 2019 -0400 |
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| @@ -0,0 +1,4 @@ +#id name species value +#biogrid_human_08-01-2019 Human (Homo sapiens) 08/01/2019 Human PPI_dictionaries/Human_biogrid.json +#biogrid_mouse_08-01-2019 Mouse (Mus musculus) 08/01/2019 Mouse PPI_dictionaries/Mouse_biogrid.json +#biogrid_rat_08-01-2019 Rat (Rattus norvegicus) 08/01/2019 Rat PPI_dictionaries/Rat_biogrid.json |
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| diff -r 000000000000 -r 9e31ea9fc7ea tool-data/proteore_bioplex_dictionaries.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_bioplex_dictionaries.loc.sample Wed Mar 13 06:30:42 2019 -0400 |
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| @@ -0,0 +1,2 @@ +#id name species value +#bioplex_human_08-01-2019 Human (Homo sapiens) 08/01/2019 Human PPI_dictionaries/human_bioplex.json |
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| diff -r 000000000000 -r 9e31ea9fc7ea tool-data/proteore_humap_dictionaries.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_humap_dictionaries.loc.sample Wed Mar 13 06:30:42 2019 -0400 |
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| @@ -0,0 +1,2 @@ +#id name species value +#humap_human_01-02-2019 Human (Homo sapiens) 01/02/19 Human PPI_dictionaries/Human_humap_01-02-2019.json |
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| diff -r 000000000000 -r 9e31ea9fc7ea tool-data/proteore_id_mapping_Human.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_id_mapping_Human.loc.sample Wed Mar 13 06:30:42 2019 -0400 |
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| @@ -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 |
| b |
| diff -r 000000000000 -r 9e31ea9fc7ea tool-data/proteore_id_mapping_Mouse.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_id_mapping_Mouse.loc.sample Wed Mar 13 06:30:42 2019 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 9e31ea9fc7ea tool-data/proteore_id_mapping_Rat.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_id_mapping_Rat.loc.sample Wed Mar 13 06:30:42 2019 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 9e31ea9fc7ea tool-data/proteore_nextprot_ref.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_nextprot_ref.loc.sample Wed Mar 13 06:30:42 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +#<id> <name> <value> +#nextprot_ref_09-03-2019 neXtProt release 09-03-2019 tool-data/nextprot_ref_09-03-2019.tsv |
| b |
| diff -r 000000000000 -r 9e31ea9fc7ea tool-data/proteore_protein_atlas_normal_tissue.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_protein_atlas_normal_tissue.loc.sample Wed Mar 13 06:30:42 2019 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 9e31ea9fc7ea tool-data/proteore_protein_atlas_tumor_tissue.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteore_protein_atlas_tumor_tissue.loc.sample Wed Mar 13 06:30:42 2019 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 9e31ea9fc7ea tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Mar 13 06:30:42 2019 -0400 |
| b |
| @@ -0,0 +1,43 @@ +<?xml version="1.0"?> +<tables> + <table name='proteore_peptide_atlas' comment_char="#"> + <columns>id, name, tissue, value</columns> + <file path="tool-data/proteore_peptide_atlas.loc"/> + </table> + <table name="proteore_protein_atlas_normal_tissue" comment_char="#"> + <columns>id, name, tissue, value</columns> + <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_Human" comment_char="#"> + <columns>id, name, species, value</columns> + <file path="tool-data/proteore_id_mapping_Human.loc" /> + </table> + <table name="proteore_id_mapping_Mouse" comment_char="#"> + <columns>id, name, species, value</columns> + <file path="tool-data/proteore_id_mapping_Mouse.loc" /> + </table> + <table name="proteore_id_mapping_Rat" comment_char="#"> + <columns>id, name, species, value</columns> + <file path="tool-data/proteore_id_mapping_Rat.loc" /> + </table> + <table name="proteore_biogrid_dictionaries" comment_char="#"> + <columns>id, name, species, value</columns> + <file path="tool-data/proteore_biogrid_dictionaries.loc" /> + </table> + <table name="proteore_bioplex_dictionaries" comment_char="#"> + <columns>id, name, species, value</columns> + <file path="tool-data/proteore_bioplex_dictionaries.loc" /> + </table> + <table name="proteore_humap_dictionaries" comment_char="#"> + <columns>id, name, species, value</columns> + <file path="tool-data/proteore_humap_dictionaries.loc" /> + </table> + <table name='proteore_nextprot_ref' comment_char="#"> + <columns>id, name, value</columns> + <file path="tool-data/proteore_nextprot_ref.loc"/> + </table> +</tables> |