comparison ivar_trim.xml @ 12:e3bb03cf207a draft

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

11:5671e1d3d5ee

<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy4" profile="21.01">
    <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 &&

            <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" />

12:e3bb03cf207a

<tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@">
    <description>Trim reads in aligned BAM</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <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 &&

            <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" ftype="bam">
                <assert_contents>
                    <has_size value="4023965" delta="1000"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="Found 68 primers in BED file"/>
                <has_text text="Using Region: PRV"/>
                <has_text text="Found 40964 mapped reads"/>
                <has_text text="reads were quality trimmed below the minimum length of 30 bp and were not written to file"/>
                <has_text text="reads that started outside of primer regions were not written to file"/>
            </assert_stdout>
        </test>
        <test>
            <conditional name="primer">
                <param name="source" value="cached" />
                <param name="cached_bed" value="SARS-CoV-2-ARTICv1" />