<tool id="rename_sequences" name="Rename sequences" version="1.0.0.3">
    <description>Rename sequences using numerical counter, keep required prefix and pair
        information
    </description>
    <requirements>
        <requirement type="package" version="3">python</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="renameSequences2.py"/>
    </required_files>
    <command>
        python '$__tool_directory__'/renameSequences2.py $input $paired index.tmp
        $prefix_length > $output
    </command>

    <inputs>
        <param format="fasta" type="data" name="input" label="Choose your FASTA file"/>
        <param name="prefix_length" type="integer" size="10" value="0"
               label="Prefix length"
               help="Enter the length of prefix to keep in sequences names"/>
        <param name="paired" type="boolean" truevalue="true" falsevalue="false"
               checked="False" label="Sequences are paired-end reads in interlaced format"
               help=""/>
    </inputs>


    <outputs>
        <data format="fasta" name="output"
              label="Renamed sequences from dataset ${input.hid}"/>
    </outputs>

    <help>
        **What is does**

        Use this tool to rename your sequences with numerical counter while keeping
        sequence name prefex as part of the name.
        If paired-end reads are used, the last character in sequence name is used to
        distinguish pairs.

    </help>
</tool>