comparison trim_galore.xml @ 13:b6c00b82f623 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit be11349529528f508eb05073396e80c3d1cbed4d

12:1bf4789584dc

<tool id="trim_galore" name="Trim Galore!" version="0.4.3.0" profile="17.01">
    <!-- Wrapper compatible with Trim Galore! version 0.4.3 -->
    <description>Quality and adapter trimmer of reads</description>
    <macros>
        <macro name="adapter_trimming">
            <conditional name="trimming">

        <requirement type="package" version="0.4.3">trim-galore</requirement>
    </requirements>
    <version_command>
        trim_galore --version
    </version_command>
    <command detect_errors="exit_code"><![CDATA[
        #set compressed = 'no'
        #if $singlePaired.sPaired == "single":
            #if $singlePaired.input_singles.is_of_type("fastq.gz"):
                #set read1 = 'input_1.fastq.gz'
                #set compressed = 'gz'

            $rrbs.rrbs
            $rrbs.non_directional
        #end if

        --output_dir ./
        --suppress_warn

        #if $params.settingsType == "custom" and not $params.report:
            --no_report_file
        #end if

            <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
            <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
            <param name="sPaired" value="paired" />
            <param name="settingsType" value="custom" />
            <param name="report" value="true" />
            <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
            <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
            <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
        </test>

        <test>
            <param name="input_mate_pairs">

            <param name="retain_unpaired_select" value="retain_unpaired_output" />

            <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />

            <output_collection name="trimmed_reads_paired_collection" type="paired">
                <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
                <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
            </output_collection>

            <output_collection name="trimmed_reads_unpaired_collection" type="paired">
                <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
                <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

13:b6c00b82f623

<tool id="trim_galore" name="Trim Galore!" version="0.4.3.1" profile="17.01">
    <!-- Wrapper compatible with Trim Galore! version 0.4.3 -->
    <description>Quality and adapter trimmer of reads</description>
    <macros>
        <macro name="adapter_trimming">
            <conditional name="trimming">

        <requirement type="package" version="0.4.3">trim-galore</requirement>
    </requirements>
    <version_command>
        trim_galore --version
    </version_command>
    <command detect_errors="aggressive"><![CDATA[
        #set compressed = 'no'
        #if $singlePaired.sPaired == "single":
            #if $singlePaired.input_singles.is_of_type("fastq.gz"):
                #set read1 = 'input_1.fastq.gz'
                #set compressed = 'gz'

            $rrbs.rrbs
            $rrbs.non_directional
        #end if

        --output_dir ./

        #if $params.settingsType == "custom" and not $params.report:
            --no_report_file
        #end if

            <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
            <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
            <param name="sPaired" value="paired" />
            <param name="settingsType" value="custom" />
            <param name="report" value="true" />
            <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
            <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
            <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
        </test>

        <test>
            <param name="input_mate_pairs">

            <param name="retain_unpaired_select" value="retain_unpaired_output" />

            <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />

            <output_collection name="trimmed_reads_paired_collection" type="paired">
                <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
                <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
            </output_collection>

            <output_collection name="trimmed_reads_unpaired_collection" type="paired">
                <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
                <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does**