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author | dchristiany |
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date | Tue, 15 Jan 2019 05:30:51 -0500 |
parents | c11d5bdc22e0 |
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<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.15.3" tool_type="manage_data"> <description> to create or update reference files for proteore tools </description> <requirements> <requirement type="package" version="3.7.1">python</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ python --version ; python $__tool_directory__/resource_building.py #if $database.database == "human_protein_atlas" --hpa "$database.tissues" #else if $database.database == "peptide_atlas" --peptideatlas="$database.tissues" #else if $database.database == "id_mapping" --id_mapping="$database.species" #else if $database.database == "PPI" --species="$database.species" --interactome="$database.interactome" #end if --output "$output" ]]></command> <inputs> <conditional name="database"> <param name="database" type="select"> <option value="human_protein_atlas">Human Protein Atlas</option> <option value="peptide_atlas">Peptide Atlas</option> <option value="id_mapping">ID mapping</option> <option value="PPI">Build protein interaction maps</option> </param> <when value="human_protein_atlas"> <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> </param> </when> <when value="peptide_atlas"> <param name="tissues" type="select" multiple="false" label="Please select the tissue"> <option value="1-Human_Liver">Human liver</option> <option value="2-Human_Brain">Human brain</option> <option value="4-Human_Heart">Human heart</option> <option value="5-Human_Kidney">Human kidney</option> <option value="10-Human_Plasma">Human blood plasma</option> <option value="13-Human_Urine">Human urine</option> <option value="24-Human_CSF">Human cerebrospinal fluid</option> </param> </when> <when value="id_mapping"> <param name="species" type="select" multiple="false" label="Please select the species"> <option value="human">Human (Homo sapiens)</option> <option value="mouse">Mouse (Mus musculus)</option> <option value="rat">Rat (Rattus norvegicus)</option> </param> </when> <when value="PPI"> <param name="interactome" type="select" multiple="false" label="Please select interactome"> <option value="biogrid">BioGRID</option> <option value="bioplex">Bioplex</option> <option value="humap">Hu.map</option> </param> <param name="species" type="select" multiple="false" label="Please select the species"> <option value="human">Human (Homo sapiens)</option> <option value="mouse">Mouse (Mus musculus)</option> <option value="rat">Rat (Rattus norvegicus)</option> </param> </when> </conditional> </inputs> <outputs> <!--data format="tabular" name="output"> <discover_datasets pattern="(?P<designation>.+).tsv" ext="tabular" visible="true" assign_primary_output="true" /> </data--> <data name="output" format="data_manager_json"/> </outputs> <tests> </tests> <help><![CDATA[ **Description** This tool is a data manager designed to update resources files of ProteoRe tools. For now, only resources files for tools listed below are handled: * "Get MS/MS observations in tissue/fluid [Peptide Atlas]" * "Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas]" * "ID converter" ----- **Input** There's no input needed, once you selected the tool and file you want to update, it will be generated automatically. ----- **Parameters** * database: the database to update (for now one per tool) Once a database is selected, there's a second dropdown menu to select the specific file you want to update. * for 'Human Protein Atlas': 'Normal tissue', 'Pathology' and 'Full Atlas' * for 'Peptide Atlas': 'Human liver', 'Human brain', 'Human heart', 'Human kidney', 'Human blood plasma', 'Human urine' and 'Human cerebrospinal fluid' * for 'ID mapping': 'Human (Homo sapiens)', 'Mouse (Mus musculus)' and 'Rat (Rattus norvegicus)' * for 'Build protein interaction maps': "BioGRID", "Bioplex" and "Human (Homo sapiens)", "Mouse (Mus musculus)", "Rat (Rattus norvegicus)" ----- **Output** The output is the reference file selected for update in input. For example, if you select database="Human Protein Atlas" and Please select tissue="Normal tissue": the output is a new reference file for "Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas]" dated from the day and listed in the dropdown menu "Normal tissue HPA version". .. class:: warningmark A reference file created with this data manager will appears in the concerned ProteoRE tool. It can not be removed with the data manager. ----- **Data sources** For 'Human Protein Atlas': * `Normal Tissue <https://www.proteinatlas.org/download/normal_tissue.tsv.zip>`_. * `Pathology <https://www.proteinatlas.org/download/pathology.tsv.zip>`_. * `Full Atlas <https://www.proteinatlas.org/download/proteinatlas.tsv.zip>`_. For 'Peptide Atlas': * `Human liver <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=1&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_. * `Human brain <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=2&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_. * `Human heart <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=3&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_. * `Human kidney <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=4&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_. * `Human plasma <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=5&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_. * `Human urine <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=6&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_. * `Human CSF <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=7&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_. For ID mapping: * `HUMAN_9606_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz>`_. * `HUMAN_9606_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz>`_. * `nextprot_ac_list_all.txt <ftp://ftp.nextprot.org/pub/current_release/ac_lists/nextprot_ac_list_all.txt>`_. * `MOUSE_10090_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping_selected.tab.gz>`_. * `MOUSE_10090_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping.dat.gz>`_. * `RAT_10116_idmapping_selected.tab <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/RAT_10116_idmapping_selected.tab.gz>`_. * `RAT_10116_idmapping.dat <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/RAT_10116_idmapping.dat.gz>`_. For Build protein interaction maps: * `BIOGRID_oragism <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.167/BIOGRID-ORGANISM-3.5.167.tab2.zip>`_. * `NCBI2Reactome.txt <https://www.reactome.org/download/current/NCBI2Reactome.txt>`_. * `Bioplex_interactionList_v4a.tsv <http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv>`_. * `UniProt2Reactome.txt <https://reactome.org/download/current/UniProt2Reactome.txt>`_. ----- .. class:: infomark **Authors** David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform This work has been partially funded through the French National Agency for Research (ANR) IFB project. Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. ]]></help> <citations> </citations> </tool>