view fastq_masker_by_quality.xml @ 2:eb592e9ec47a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a

<tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.1.1">
    <description>by quality score</description>
    <requirements>
        <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
    </requirements>
    <command><![CDATA[
gx-fastq-masker-by-quality '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s ${quality_score} -c ${score_comparison}
#if $mask_type.value == 'lowercase'
    --lowercase
#else
    -m ${mask_type}
#end if
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="File to mask" />
        <param name="mask_type" type="select" label="Mask input with">
            <option value="N">N's</option>
            <option value="lowercase">Lowercase</option>
        </param>
        <param name="score_comparison" type="select" label="When score is">
            <option value="le" selected="true">Less than or equal</option>
            <option value="lt">Less than</option>
            <option value="eq">Equal to</option>
            <option value="ne">Not Equal to</option>
            <option value="ge">Greater than</option>
            <option value="gt">Greater than or equal</option>
        </param>
        <param name="quality_score" type="integer" value="0" label="Quality score"/>
    </inputs>
    <outputs>
        <data name="output_file" format_source="input_file" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
            <param name="mask_type" value="N" />
            <param name="score_comparison" value="le" />
            <param name="quality_score" value="20" />
            <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" ftype="fastqsanger" />
        </test>
        <test>
            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
            <param name="mask_type" value="lowercase" />
            <param name="score_comparison" value="le" />
            <param name="quality_score" value="20" />
            <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" ftype="fastqsanger" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method.

This tool is not available for use on color space (csSanger) formats.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq281</citation>
    </citations>
</tool>