comparison ivar_removereads.xml @ 11:7f1cfa4c0e32 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324

10:ee29337f905c

<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy3" profile="21.01">
    <description>Remove reads from trimmed BAM file</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[
        cp '$input_bed' binding_sites.bed &&
        python '$__tool_directory__/sanitize_bed.py' binding_sites.bed &&
        #if $amplicons.computed == "yes"
            python '$__tool_directory__/write_amplicon_info_file.py' binding_sites.bed amplicon_info.tsv &&

        -t masked_primers.txt
    ]]></command>
    <inputs>
        <param name="input_bam" argument="-i" type="data" format="bam"
        label="Bam input"
        help="BAM dataset, preprocessed with ivar trim, to remove reads from" />
        <param name="variants_tsv" type="data" format="tabular"
        label="Variants input"
        help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS." />
        <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information"
        help="The same six-column BED dataset that served as input to ivar trim"/>
        <conditional name="amplicons">
            <param name="computed" type="select" label="Compute amplicon info from BED file" help="For suitable primer binding site datasets amplicon info can be computed directly (see tool help below). For others you will need to provide an extra amplicon info dataset.">
                <option value="yes" selected="true">Yes</option>

        <test>
            <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
            <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
            <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
            <conditional name="amplicons">
                <param name="computed" value="no" />
                <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
            </conditional>
            <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
        </test>
        <test>
            <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
            <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
            <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
            <conditional name="amplicons">
                <param name="computed" value="yes" />
            </conditional>
            <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
        </test>
    </tests>
    <help><![CDATA[
This Galaxy tool combines the functionality of ``ivar getmasked`` and
``ivar removereads``. No separate ``ivar getmasked`` step is required when

11:7f1cfa4c0e32

<tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
    <description>Remove reads from trimmed BAM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
        cp '$input_bed' binding_sites.bed &&
        python '$__tool_directory__/sanitize_bed.py' binding_sites.bed &&
        #if $amplicons.computed == "yes"
            python '$__tool_directory__/write_amplicon_info_file.py' binding_sites.bed amplicon_info.tsv &&

        -t masked_primers.txt
    ]]></command>
    <inputs>
        <param name="input_bam" argument="-i" type="data" format="bam"
        label="Bam input"
        help="BAM dataset, preprocessed with ivar trim, to remove reads from"/>
        <param name="variants_tsv" type="data" format="tabular"
        label="Variants input"
        help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS."/>
        <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information"
        help="The same six-column BED dataset that served as input to ivar trim"/>
        <conditional name="amplicons">
            <param name="computed" type="select" label="Compute amplicon info from BED file" help="For suitable primer binding site datasets amplicon info can be computed directly (see tool help below). For others you will need to provide an extra amplicon info dataset.">
                <option value="yes" selected="true">Yes</option>

        <test>
            <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
            <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
            <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
            <conditional name="amplicons">
                <param name="computed" value="no"/>
                <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
            </conditional>
            <output name="output_bam" ftype="bam">
                <assert_contents>
                    <has_size value="3185672" delta="1000"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
            <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
            <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
            <conditional name="amplicons">
                <param name="computed" value="yes"/>
            </conditional>
            <output name="output_bam" ftype="bam">
                <assert_contents>
                    <has_size value="3185672" delta="1000"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This Galaxy tool combines the functionality of ``ivar getmasked`` and
``ivar removereads``. No separate ``ivar getmasked`` step is required when