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author dchristiany
date Tue, 15 Jan 2019 10:00:02 -0500
parents 85532a48e4e4
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<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.15.5" tool_type="manage_data">
<description>
to create or update reference files for proteore tools
</description>
<requirements>
</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"
    #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&lt;designation&gt;.+).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>