<tool id="names_affixer" name="FASTQ Read name affixer" version="1.0.0.4">
    <description>Tool appending suffix and prefix to sequences names</description>
    <requirements>
        <requirement type="package" version="3">python</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="name_affixer.py"/>
    </required_files>
    <command>
        python ${__tool_directory__}/name_affixer.py -f $input -p "$prefix" -s "$suffix" -n
        $nspace > $output
    </command>

    <inputs>
        <param format="fastq" type="data" name="input" label="Choose your FASTQ file"/>
        <param name="prefix" type="text" size="10" value="" label="Prefix"
               help="Enter prefix which will be added to all sequences names"/>
        <param name="suffix" type="text" size="10" value="" label="Suffix"
               help="Enter suffix which will be added to all sequences names"/>
        <param name="nspace" type="integer" size="10" value="0" min="0" max="1000"
               label="Number of spaces in sequence name to ignore"
               help="Sequence name is a string before the first space. If you want name to include spaces in name, enter positive integer. All other characters beyond ignored spaces are omitted"/>
    </inputs>


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

    <help>
        **What is does**

        Tool for appending prefix and suffix to sequences names in fastq formated
        sequences.

        **Example**

        The following Solexa-FASTQ file:

        ::

        @CSHL_4_FC042GAMMII_2_1_517_596
        GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
        +CSHL_4_FC042GAMMII_2_1_517_596
        40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24
        24 9 24 9 40 10 10 15 40

        is renamed to:

        ::

        @prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
        GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
        +prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
        40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24
        24 9 24 9 40 10 10 15 40

        different format:


        ::

        @HISEQ1:92:c0190acxx:8:1101:1252:2230 2:N:0:CGATGT
        AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
        +
        CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9

        is renamed to:

        ::

        @prefixHISEQ1:92:c0190acxx:8:1101:1252:2230suffix
        AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
        +
        CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9

        note that string after first space is omitted!

        Because sequence names sometimes containg spaces which delimit the actual name. 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
        +
        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG

        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
        +
        IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG


    </help>
</tool>