<tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1">
  <description>builder</description>
  <requirements>
    <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>
  </requirements>
  <stdio>
    <exit_code range=":-1" />
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
    Rscript --vanilla '$__tool_directory__/customProDB_annotation.R'
    --outputFile '${out_file}'
    --dbkey '${dbkey}'
    --dbsnp '${dbsnp}'
    $cosmic
    --dbkey_description '${ dbkey.get_display_text() }'
    2>1
]]>
  </command>
  <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" truevalue="--cosmic true" falsevalue="" 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>