annotate ivar_trim.xml @ 4:db536ad45f28 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"

<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy1">
    <description>Trim reads in aligned BAM</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.8.1">python</requirement>
    </expand>
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #if $primer.source == "history"
            cp '$primer.input_bed' bed.bed &&
        #else
            cp '$primer.cached_bed.fields.path' bed.bed &&
        #end if
        python '$__tool_directory__/sanitize_bed.py' bed.bed &&

        ln -s '$input_bam' sorted.bam &&
        ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&

        ivar trim
        -i sorted.bam
        -b bed.bed
        -m $min_len
        -q $min_qual
        -s $window_width
        $inc_primers
        -p trimmed &&
        samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam
    ]]>    </command>
    <inputs>
        <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
        <conditional name="primer">
            <param label="Source of primer information" name="source" type="select">
                <option value="history" selected="true">History</option>
                <option value="cached">Built-in</option>
            </param>
            <when value="history">
                <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
            </when>
            <when value="cached">
                <param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list">
                    <options from_data_table="primer_scheme_bedfiles">
                        <filter type="sort_by" column="1" />
                    <validator type="no_options" message="No primer schemes are available" />
                    </options>
                </param>
            </when>
        </conditional>
        <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/>
        <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/>
        <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/>
        <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads with no primers"/>
    </inputs>
    <outputs>
        <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/>
    </outputs>
    <tests>
        <!-- #1: SARS-Cov data-->
        <test>
            <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
            <param name="input_bed" value="covid19/ARTIC-V1.bed" />
            <param name="inc_primers" value="true" />
            <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
        </test>
        <test>
            <!-- Test with primer bed file that needs to be sanitized -->
            <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
            <param name="input_bed" value="covid19/ARTIC-V1-bad.bed" />
            <param name="inc_primers" value="true" />
            <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
        </test>
        <!-- #1: Zika data-->
        <test>
            <conditional name="primer">
                <param name="source" value="history" />
                <param name="input_bed" value="zika/db/zika_primers.bed" />
            </conditional>
            <param name="input_bam" value="zika/Z52_a.sorted.bam" />
            <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
        </test>
        <test>
            <conditional name="primer">
                <param name="source" value="history" />
                <param name="input_bed" value="zika/db/zika_primers.bed" />
            </conditional>
            <param name="input_bam" value="zika/Z52_b.sorted.bam" />
            <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
        </test>
        <test>
            <conditional name="primer">
                <param name="source" value="cached" />
                <param name="cached_bed" value="SARS-CoV-2-ARTICv1" />
            </conditional>
            <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
            <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" />
        </test>
    </tests>
    <help><![CDATA[
        iVar uses primer positions supplied in a BED file to soft clip primer
        sequences from an aligned and sorted BAM file. Following this, the reads are
        trimmed based on a quality threshold(Default: 20). To do the quality
        trimming, iVar uses a sliding window approach(Default: 4). The windows
        slides from the 5' end to the 3' end and if at any point the average base
        quality in the window falls below the threshold, the remaining read is soft
        clipped. If after trimming, the length of the read is greater than the
        minimum length specified(Default: 30), the read is written to the new
        trimmed BAM file
        
        Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
    ]]>    </help>
    <expand macro="citations" />
</tool>