view data_manager/customProDB_annotation.xml @ 5:a0ca66b32792 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty

<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>
</tool>