comparison ivar_trim.xml @ 8:397e5f0eb3ef draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"

7:364f4ffec275

<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy0">
    <description>Trim reads in aligned BAM</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

            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 &&
        #if $amplicons.filter_by == 'yes'
            python '$__tool_directory__/prepare_amplicon_info.py' bed.bed '$amplicons.amplicon_info' amplicon_info.tsv &&
        #end if
        ln -s '$input_bam' sorted.bam &&
        ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&

        ivar trim

            </when>
        </conditional>
        <conditional name="amplicons">
            <param name="filter_by" type="select"
            label="Filter reads based on amplicon info"
            help="When you select Yes you will need to provide an additional amplicon info dataset. Reads that are not fully contained in any amplicon will be dropped before primer trimming. This option is currently marked as [Experimental] in ivar, but nevertheless recommended here.">
                <option value="">No, allow reads to extend beyond amplicon boundaries</option>
                <option value="yes">Yes, drop reads that extend beyond amplicon boundaries</option>
            </param>
            <when value="yes">
                <param name="amplicon_info" argument="-f" type="data" format="tabular" />
            </when>
            <when value="" />
        </conditional>

                <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" compare="sim_size" delta="100000"/>
        </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 further based on a quality threshold.

8:397e5f0eb3ef

<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">

            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 &&
        #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_computed'
            #if $amplicons.filter_by == 'yes_computed':
                python '$__tool_directory__/write_amplicon_info_file.py' bed.bed amplicon_info_raw.tsv &&
            #else
                ln -s '$amplicons.amplicon_info' amplicon_info_raw.tsv &&
            #end if
            python '$__tool_directory__/prepare_amplicon_info.py' bed.bed amplicon_info_raw.tsv amplicon_info.tsv &&
        #end if
        ln -s '$input_bam' sorted.bam &&
        ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&

        ivar trim

            </when>
        </conditional>
        <conditional name="amplicons">
            <param name="filter_by" type="select"
            label="Filter reads based on amplicon info"
            help="When you select Yes reads that are not fully contained in any amplicon will be dropped before primer trimming. Info on amplicons can be computed from the primer BED file or provided by the user. This option is currently marked as [Experimental] in ivar, but nevertheless recommended here.">
                <option value="">No, allow reads to extend beyond amplicon boundaries</option>
                <option value="yes_compute">Yes, drop reads that extend beyond amplicon boundaries</option>
                <option value="yes">Yes, drop reads that extend beyond amplicon boundaries and use my amplicon info file</option>
            </param>
            <when value="yes_compute" />
            <when value="yes">
                <param name="amplicon_info" argument="-f" type="data" format="tabular" />
            </when>
            <when value="" />
        </conditional>

                <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" 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>
            <conditional name="amplicons">
                <param name="filter_by" value="yes_compute" />
            </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" compare="sim_size" delta="100000"/>
        </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 further based on a quality threshold.