<tool id="fasta_affixer" name="FASTA read name affixer" version="1.0.0.3">
    <description>Appending suffix and prefix to the read names</description>
    <required_files>
        <include type="literal" path="fasta_affixer.py"/>
    </required_files>

    <command>
        python '$__tool_directory__'/fasta_affixer.py -f $input -p "$prefix" -s "$suffix"
        -n $nspace -o $output
    </command>

    <inputs>
        <param format="fasta" type="data" name="input" label="Choose your FASTA file"/>
        <param name="prefix" type="text" size="10" value="" label="Prefix"
               help="Enter prefix which will be added to all read names"/>
        <param name="suffix" type="text" size="10" value="" label="Suffix"
               help="Enter suffix which will be added to all read names"/>
        <param name="nspace" type="integer" size="10" value="0" min="0" max="1000"
               label="Number of spaces in the name to ignore"
               help="By default, a string before the first space is considered to be the read name, and all characters following the space are discarded. If you want to keep the information following the space(s) in the name, enter positive integer."/>
    </inputs>

    <outputs>
        <data format="fasta" name="output"
              label="FASTA dataset ${input.hid} with modified sequence names"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="single_output.fasta"/>
            <param name="prefix" value="TEST"/>
            <param name="suffux" value="OK"/>
            <param name="nspace" value="0"/>
            <output name="output" value="prefix_suffix.fasta"/>
        </test>
    </tests>
    <help>
        **What is does**

        Tool for appending prefix and suffix to sequences names in fasta formated
        sequences. This tool is useful
        if you want to do comparative analysis with RepeatExplorer and need to
        append sample codes to sequence identifiers

        **Example**
        The following fasta file:

        ::

        >123454
        acgtactgactagccatgacg
        >234235
        acgtactgactagccatgacg

        is renamed to:

        ::

        >prefix123454suffix
        acgtactgactagccatgacg
        >prefix234235suffix
        acgtactgactagccatgacg


        By default, anything after spaces is
        excluded from sequences name. In example sequence:

        ::

        >SRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1
        CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG

        when **Number of spaces in name to ignore** is set to 0 (default) the output will
        be:

        ::

        >prefixSRR352150.23846180suffix
        CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC


        If you want to keep spaces the setting **Number of spaces in name to ignore** to 1
        will yield

        ::

        >prefixSRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1suffix
        CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC


    </help>
</tool>