Mercurial > repos > proteore > proteore_data_manager
diff data_manager/resource_building.xml @ 0:9e31ea9fc7ea draft
planemo upload commit 567ba7934c0ca55529dfeb5e7ca0935ace260ad7-dirty
author | proteore |
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date | Wed, 13 Mar 2019 06:30:42 -0400 |
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children | f3507260b30f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/resource_building.xml Wed Mar 13 06:30:42 2019 -0400 @@ -0,0 +1,223 @@ +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.13" tool_type="manage_data"> +<description> +to create or update reference files for proteore tools +</description> +<requirements> + <!--requirement type="package" version="1.8.2">sparqlwrapper</requirement--> +</requirements> +<stdio> + <exit_code range="1:" /> +</stdio> +<command><![CDATA[ + + python $__tool_directory__/resource_building.py + #if $database.database == "human_protein_atlas" + --hpa "$database.tissues" + #else if $database.database == "peptide_atlas" + --peptideatlas="$database.tissues" + --date="$database.date" + #else if $database.database == "id_mapping" + --id_mapping="$database.species" + #else if $database.database == "PPI" + --interactome="$database.base.interactome" + #if $database.base.interactome == "biogrid" + --species="$database.base.species" + #end if + #else if $database.database == "nextprot" + --database=$database.database + #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> + <option value="nextprot">neXtProt</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="432.Human_Adrenal_gland">Human Adrenal gland proteome</option> + <option value="441.Human_Brain">Human Brain proteome</option> + <option value="427.Human_Breast">Human Breast proteome</option> + <option value="434.Human_CSF">Human CSF (Cerebro Spinal Fluid) proteome</option> + <option value="374.Human_Colon_cancer">Human Colon cancer proteome</option> + <option value="429.Human_Digestive_system">Human Digestive system proteome</option> + <option value="430.Human_Female_reproductive_system">Human Female reproductive system proteome</option> + <option value="418.Human_Heart">Human Heart proteome</option> + <option value="424.Human_Kidney">Human Kidney proteome</option> + <option value="425.Human_Liver">Human Liver proteome</option> + <option value="419.Human_Lung">Human Lung proteome</option> + <option value="431.Human_Male_reproductive_system">Human Male reproductive system proteome</option> + <option value="420.Human_Pancreas">Human Pancreas proteome</option> + <option value="465.Human_Plasma_non_glyco">Human Plasma non glyco proteome</option> + <option value="421.Human_Spleen">Human Spleen proteome</option> + <option value="463.Human_Testis">Human Testis proteome</option> + <option value="422.Human_Urinary_bladder">Human Bladder proteome</option> + <option value="423.Human_Urine">Human Urine proteome</option> + </param> + <param name="date" type="text" value="" label="enter the build date" help="for example: '2018-04'"/> + </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"> + <conditional name="base"> + <param name="interactome" type="select" multiple="false" label="Please select interactome"> + <option value="biogrid">BioGRID</option> + <option value="bioplex">Human Bioplex 2.0</option> + <option value="humap">Human protein complex Map (Hu.map)</option> + </param> + <when value="biogrid"> + <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="bioplex"/> + <when value="humap"/> + </conditional> + </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 Adrenal gland proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=432&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>`_. +* `Human Brain proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=441&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>`_. +* `Human Breast Proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=427&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>`_. +* `Human CSF proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=434&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>`_. +* `Human Digestive System proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=429&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>`_. +* `Human female reproductive system proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=430&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>`_. +* `Human Heart proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=418&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>`_. +* `Human Kidney man Kidney Proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=424&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>`_. +* `Human Liver proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=425&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>`_. +* `Human Lung proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=419&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>`_. +* `Human Male Reproductive System proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=431&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>`_. +* `Human Pancreas proteome <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=420&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>`_. +* `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>`_. +* `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>`_. +* `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>`_. +* `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>`_. +* `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>`_. + +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>