view data_manager/resource_building.xml @ 2:1f1fb404255a draft

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<tool id="data_manager_proteore" name="Get source files for proteore tools" version="0.1" 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"
    #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>
        </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">Homo sapiens</option>
                <option value="mouse">Mus musculus</option>
                <option value="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[

TODO

-----

.. class:: infomark

**Authors**

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 [e-mail] for any questions or concerns about the Galaxy implementation of this tool.
 
    ]]></help>
    <citations>
    </citations>

</tool>