comparison filtlong.xml @ 1:8880fb74ef56 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 914aebf765a006b3d284388aba0584d0035a8a66

0:a64b45c8b174

        --window_size '$other.window_size'
    #end if
    '$input_file' > output.fastq
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastq" label="Input FASTQ" help="FASTQ of input reads"/>
        <section name="output_thresholds" title="Output thresholds">
            <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/>
            <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/>
            <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/>
            <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
            <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
        </section>
        <section name="external_references" title="External references">
            <param argument="--assembly" type="data" format="fasta" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
            <param argument="--illumina_1" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
            <param argument="--illumina_2" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
        </section>
        <section name="score_weights" title="Score weights">
            <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/>
            <param argument="--mean_q_weight" type="float" min="0" value="1" optional="True" label="Weight mean quality" help="Weight given to the mean quality score (default: 1)"/>
            <param argument="--window_q_weight" type="float" min="0" value="1" optional="True" label="Weight window quality" help="Weight given to the window quality score (default: 1)"/>

        <section name="other" title="Other">
            <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/>
        </section>
    </inputs>
    <outputs>
        <data name="outfile" format="fastq" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fastq" value="test.fastq"/>
            <param name="min_length" value="1000"/>
            <param name="keep_percent" value="50"/>
            <param name="target_bases" value="500000000"/>
            <output name="outfile" ftype="fastq" file="output.fastq"/>
        </test>
        <test>
            <param name="input_file" ftype="fastq" value="test_reference.fasta"/>
            <param name="illumina_1" ftype="fastq.gz" value="test_reference_1.fastq.gz"/>
            <param name="illumina_2" ftype="fastq.gz" value="test_reference_2.fastq.gz"/>
            <param name="min_length" value="1000"/>
            <param name="keep_percent" value="90"/>
            <param name="target_bases" value="500000000"/>
            <param name="trim" value="True"/>
            <param name="split" value="500"/>
            <output name="outfile" ftype="fastq" file="output_reference.fastq"/>
        </test>
    </tests>
    <help><![CDATA[
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
    ]]></help>

1:8880fb74ef56

        --window_size '$other.window_size'
    #end if
    '$input_file' > output.fastq
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger" label="Input FASTQ" help="FASTQ of input reads"/>
        <section name="output_thresholds" title="Output thresholds">
            <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/>
            <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/>
            <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/>
            <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
            <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
        </section>
        <section name="external_references" title="External references">
            <param argument="--assembly" type="data" format="fasta" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
            <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
            <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
        </section>
        <section name="score_weights" title="Score weights">
            <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/>
            <param argument="--mean_q_weight" type="float" min="0" value="1" optional="True" label="Weight mean quality" help="Weight given to the mean quality score (default: 1)"/>
            <param argument="--window_q_weight" type="float" min="0" value="1" optional="True" label="Weight window quality" help="Weight given to the window quality score (default: 1)"/>

        <section name="other" title="Other">
            <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/>
        </section>
    </inputs>
    <outputs>
        <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fastqsanger" value="test.fastq"/>
            <param name="min_length" value="1000"/>
            <param name="keep_percent" value="50"/>
            <param name="target_bases" value="500000000"/>
            <output name="outfile" ftype="fastqsanger" file="output.fastq"/>
        </test>
        <test>
            <param name="input_file" ftype="fastqsanger" value="test_reference.fasta"/>
            <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/>
            <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/>
            <param name="min_length" value="1000"/>
            <param name="keep_percent" value="90"/>
            <param name="target_bases" value="500000000"/>
            <param name="trim" value="True"/>
            <param name="split" value="500"/>
            <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/>
        </test>
    </tests>
    <help><![CDATA[
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
    ]]></help>