comparison ivar_trim.xml @ 10:9f978da6528a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27f076c829f3b79c170cad55fc19e2f48c8b22ed"

9:c092052ed673

<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy2">
    <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 &&
        #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 &&

            </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

10:9f978da6528a

<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy3">
    <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>
        <requirement type="package" version="1.15">samtools</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 &&
        #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute'
            #if $amplicons.filter_by == 'yes_compute':
                python '$__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 &&

            </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" />
            <assert_command>
                <has_text text="write_amplicon_info_file" />
            </assert_command>
            <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