<tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1">
    <description>builder</description>
    <command interpreter="Rscript --vanilla">customProDB_annotation.R
      --outputFile "${out_file}"
      --dbkey "${dbkey}"
      --dbsnp "${dbsnp}"
      #if $cosmic
            --cosmic true
      #end if
      --dbkey_description ${ dbkey.get_display_text() }
      2&gt;&amp;1
    </command>
    <stdio>
        <exit_code range=":-1" />
        <exit_code range="1:" />
    </stdio>
    <inputs>
        <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" />
        <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" />
        <param type="boolean" name="cosmic" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>

    <help>

.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically. 

    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt543</citation>
        <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
                                      year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
    </citations>
</tool>