comparison trim_galore.xml @ 14:949f01671246 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5

13:b6c00b82f623

        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
            <param name="sPaired" value="single" />
            <param name="settingsType" value="custom" />
            <param name="report" value="true" />
            <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
            <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="9" />
        </test>

        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />

        </test>
        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
            <param name="sPaired" value="single" />
            <param name="trimming_select" value="--illumina" />
            <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
        </test>

        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
            <param name="sPaired" value="single" />

        </test>
        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
            <param name="sPaired" value="single" />
            <param name="adapter" value="AAAGAGC" />
            <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
        </test>

        <test>
            <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
            <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />

            <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**

14:949f01671246

        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
            <param name="sPaired" value="single" />
            <param name="settingsType" value="custom" />
            <param name="report" value="true" />
            <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
            <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="9" />
        </test>

        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />

        </test>
        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
            <param name="sPaired" value="single" />
            <param name="trimming_select" value="--illumina" />
            <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
        </test>

        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
            <param name="sPaired" value="single" />

        </test>
        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
            <param name="sPaired" value="single" />
            <param name="adapter" value="AAAGAGC" />
            <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
        </test>

        <test>
            <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
            <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />

            <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" decompress="true" />
            <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
            <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" decompress="true" />
                <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
            </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" decompress="true" />
                <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does**