annotate data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 9:4d3eff1bc421 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit d95d06f8cad152876ce15713c65099db116f8ace"

<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.4" tool_type="manage_data" profile="19.01">
    <description>fetching</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       python '$__tool_directory__/data_manager_fetch_genome_all_fasta_dbkeys.py'
       '${out_file}'
       #if str( $dbkey_source.dbkey_source_selector ) == 'existing':
           --dbkey_description '${dbkey_source.dbkey}'
       #else
           --dbkey_description '${ dbkey_source.dbkey_name or $dbkey_source.dbkey }'
       #end if
    ]]></command>
    <inputs>
        <conditional name="dbkey_source">
            <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one.">
                <option value="existing" selected="True">Existing</option>
                <option value="new">New</option>
            </param>
            <when value="existing">
                <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
            </when>
            <when value="new">
                <param name="dbkey" type="text" value="" optional="false" label="dbkey" />
                <param name="dbkey_name" type="text" value="" label="Display name for dbkey" />
            </when>
        </conditional>
        <param name="sequence_name" type="text" value="" label="Name of sequence" />
        <param name="sequence_id" type="text" value="" label="ID for sequence" />
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                <option value="ucsc" selected="True">UCSC</option>
                <option value="ncbi">NCBI</option>
                <option value="url">URL</option>
                <option value="history">History</option>
                <option value="directory">Directory on Server</option>
            </param>
            <when value="ucsc">
                <param name="requested_dbkey" type="text" value="" optional="false" label="UCSC's DBKEY for source FASTA" />
            </when>
            <when value="ncbi">
                <param name="requested_identifier" type="text" value="" optional="false" label="NCBI identifier/accession" help="Identifiers (e.g 667699573) or accessions (e.g AC020606.7) may be used" />
            </when>
            <when value="url">
                <param name="user_url" type="text" area="True" value="http://" optional="false" label="URLs" />
            </when>
            <when value="history">
                <param name="input_fasta" type="data" format="fasta" label="FASTA file" />
            </when>
            <when value="directory">
                <param name="fasta_filename" type="text" value="" optional="false" label="Full path to FASTA file on disk" />
                <param name="create_symlink" type="boolean" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" />
            </when>
        </conditional>
        <conditional name="sorting">
            <param name="sort_selector" type="select" label="Sort by chromosome name">
                <option value="as_is" selected="True">As is</option>
                <option value="lexicographical">Lexicographical</option>
                <option value="gatk">GATK</option>
                <option value="custom">Custom</option>
            </param>
            <when value="as_is" />
            <when value="lexicographical" />
            <when value="gatk" />
            <when value="custom">
                <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1">
                    <param name="identifier" type="text" value="" optional="false" label="Sequence Identifier" />
                </repeat>
                <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers">
                    <option value="discard" selected="True">Discard</option>
                    <option value="keep_append">Keep and Append</option>
                    <option value="keep_prepend">Keep and Prepend</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <!-- TODO: need some way to test that new entry was added to data table -->
        <test>
            <param name="dbkey" value="phiX174"/>
            <param name="dbkey_source|dbkey_source_selector" value="new"/>
            <param name="sequence_name" value="phiX174 sequence name"/>
            <param name="sequence_id" value="phix174"/>
            <param name="reference_source_selector" value="history"/>
            <param name="input_fasta" value="phiX174.fasta"/>
            <param name="sort_selector" value="as_is"/>
            <output name="out_file" file="phiX174.data_manager_json"/>
        </test>
    </tests>
    <help>
**What it does**

Fetches a reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table.

------

.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
    </help>
</tool>