<tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0.4">
    <description>Join pared reads into single file</description>
    <requirements>
        <container type="package" version="3">python</container>
    </requirements>
    <required_files>
        <include type="literal" path="fasta_interlacer.py"/>
    </required_files>
    <command>
        python '$__tool_directory__'/fasta_interlacer.py -a $A -b $B -p $paired -x $single
    </command>

    <inputs>
        <param format="fasta" type="data" name="A" label="Left-hand mates"/>
        <param format="fasta" type="data" name="B" label="Right-hand mates"/>
    </inputs>


    <outputs>
        <data format="fasta" name="paired"
              label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/>
        <data format="fasta" name="single"
              label="Reads without corresponding mate from datasets ${A.hid} and ${B.hid}"/>
    </outputs>

    <help>
        **What it does**
        This tools joins paired end FASTA reads from separate files, one with the left
        mates and one with the right mates, into a single files.
        Last character in identifiers is used to distinguish pairs.

        **Note !!!**
        This tools is to be used as more efficient replacement of FASTQ interlacer. Galaxy
        built-in FASTQ interlacer allows different ordering
        of sequences in both files but this flexibility comes with high memory
        requirements when large files are used. FASTA interlacer is simple but order of
        magnitude
        faster tools which can be used on files where reads are in the same order.


    </help>
</tool>