view data_manager/fetch_refseq.xml @ 6:7226cda27b03 draft

planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty

<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.7" tool_type="manage_data">
    <description>Fetch FASTA data from NCBI RefSeq and update all_fasta data table</description>
    <requirements>
        <requirement type="package" version="3">python</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
    python3 $__tool_directory__/fetch_refseq.py
      #if str( $advanced.advanced_selector ) == 'advanced':
        '${advanced.compress}'
      #end if
      --galaxy_datamanager_filename '${output_file}'
      --division_names ${division_names}
      --mol_types ${mol_types}
      #if str( $pin_date ) != 'NO':
        --pin_date '${pin_date}'
      #end if
    ]]></command>
    <inputs>
        <param argument="division_names" type="select" label="RefSeq division" multiple="true">
            <option value="archea">Archea</option>
            <option value="bacteria">Bacteria</option>
            <option value="complete">Complete</option>
            <option value="fungi">Fungi</option>
            <option value="invertebrate">Invertebrate</option>
            <option value="mitochondrion">Mitochondrion</option>
            <option value="other">Other</option>
            <option value="plant">Plant</option>
            <option value="plasmid">Plasmid</option>
            <option value="plastid">Plastid</option>
            <option value="protozoa">Protozoa</option>
            <option value="vertebrate_mammalian">Mammalian Vertebrate</option>
            <option value="vertebrate_other">Other Vertebrate</option>
            <option value="viral">Viral</option>
        </param>
        <param argument="mol_types" type="select" label="Molecule type" help="Select at least one of genomic, protein or rna sequence">
            <option value="protein">Protein</option>
            <option value="genomic">Genomic (DNA)</option>
            <option value="rna">RNA</option>
        </param>
        <conditional name="advanced">
            <param name="advanced_selector" type="select" label="Advanced Options">
                <option value="basic" selected="True">Basic</option>
                <option value="advanced">Advanced</option>
            </param>
            <when value="basic">
            </when>
            <when value="advanced">
                <param type="boolean" argument="--compress" truevalue="--compress" falsevalue="" label="Compress FASTA files" 
                    help="Compress downloaded FASTA files (with gzip). Limits compatibility with tools expecting uncompressed FASTA."/>
            </when>
        </conditional>
        <param argument="--pin_date" type="hidden" value="NO" help="Used for testing"/>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="division_names" value="plastid"/>
            <param name="mol_types" value="protein"/>
            <param name="pin_date" value="2018-03-14"/>            
            <param name="advanced_selector" value="basic"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="2018-03-14"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This data manager fetches FASTA format collections of proteins, nucleotides (genomic DNA) and RNA
from NCBI's RefSeq_ data collection.

RefSeq is released every two months and consists of a number of divisions. Some sequences are shared
between multiple divisions. This data manager allows the Galaxy administrator to select which
divisions and which molecule types within each division to download. Once downloaded the
files are made accessible by adding an entry into the *all_fasta* data table.

.. _RefSeq: https://www.ncbi.nlm.nih.gov/refseq/
    ]]>
    </help>
    <citations>
        <citation type="doi">10.1093/nar/gkv1189</citation>
    </citations>
</tool>