<tool id="data_manager_fetch_tx2gene" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data">
    <description>fetching</description>
    <requirements>
        <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement>
        <requirement type="package">r-getopt</requirement>
    </requirements>

    <command><![CDATA[
       python "$__tool_directory__"/data_manager_fetch_tx2gene.py "${out_file}"
       --type $file_type
       --dbkey_description ${ dbkey.get_display_text() }
       --base_dir $__tool_directory__
        
    ]]></command>
    <inputs>
 
        <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
        <param type="text" name="sequence_name" value="" label="Name of sequence" />
        <param type="text" name="sequence_id" value="" label="ID for sequence" />
 
        <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)">
                <option value="gtf">GTF file</option>
                <option value="gff3">GFF3 file</option>
                <option value="tx2gene">tx2gene</option>
        </param>
	<conditional name="reference_source">
	    <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
		<option value="url">URL</option>
		<option value="history">History</option>
		<option value="directory">Directory on Server</option>
	    </param>
	    <when value="url">
		<param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
	    </when>
	    <when value="history">
		<param name="input_fasta" type="data" label="File from History" multiple="False" optional="False" />
	    </when>
	    <when value="directory">
		<param type="text" name="filename" value="" label="Full path to File on disk" optional="False" />
		<param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" />
	    </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="anoGam1"/>
            <param name="sequence_name" value=""/>
            <param name="sequence_desc" value=""/>
            <param name="sequence_id" value=""/>
            <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 gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table.

------



.. class:: infomark

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

    </help>
</tool>