comparison fastq_trimmer.xml @ 3:2d0d13b0b0f1 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit bb546ea5ff3b35ea76feb0c26470e7b422d2d493

2:430b9da91435

    </requirements>
    <command><![CDATA[
gx-fastq-trimmer '$input_file' '$output_file' ${offset_type['left_column_offset']} ${offset_type['right_column_offset']} ${offset_type['base_offset_type']} '${input_file.extension[len('fastq'):]}' $keep_zero_length
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz" label="FASTQ file"/>
        <conditional name="offset_type">
            <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)&lt;br&gt;Use Percentage for variable length reads (Roche/454)">
                <option value="offsets_absolute" selected="true">Absolute Values</option>
                <option value="offsets_percent">Percentage of Read Length</option>
            </param>

3:2d0d13b0b0f1

    </requirements>
    <command><![CDATA[
gx-fastq-trimmer '$input_file' '$output_file' ${offset_type['left_column_offset']} ${offset_type['right_column_offset']} ${offset_type['base_offset_type']} '${input_file.extension[len('fastq'):]}' $keep_zero_length
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ file"/>
        <conditional name="offset_type">
            <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)&lt;br&gt;Use Percentage for variable length reads (Roche/454)">
                <option value="offsets_absolute" selected="true">Absolute Values</option>
                <option value="offsets_percent">Percentage of Read Length</option>
            </param>