comparison coverm_contig.xml @ 4:1dcea261abbe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5

3:c2a5823e4763

        </test>
        <test expect_num_outputs="1">
            <conditional name="mapped">
                <param name="mapped" value="not-mapped" />
                <conditional name="mode">
                    <param name="mode" value="co"/>
                    <conditional name="read_type">
                        <param name="type" value="single"/>
                        <param name="single" value="bad_reads.interleaved.fq"/>
                    </conditional>

4:1dcea261abbe

        </test>
        <test expect_num_outputs="1">
            <conditional name="mapped">
                <param name="mapped" value="not-mapped" />
                <conditional name="mode">
                    <param name="mode" value="individual"/>
                    <conditional name="read_type">
                        <param name="type" value="paired_collection"/>
                        <param name="paired_reads">
                            <collection type="paired">
                                <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/>
                                <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/>
                            </collection>
                        </param>
                    </conditional>
                    <param name="reference" value="7seqs.fna" />
                    <param name="sharded" value="" />
                </conditional>
            </conditional>
            <section name="alignment">
                <param name="min_read_aligned_length" value="0" />
                <param name="min_read_percent_identity" value="0" />
                <param name="min_read_aligned_percent" value="0" />
                <conditional name="proper_pairs_only">
                    <param name="proper_pairs_only" value=""/>
                </conditional>
                <param name="exclude_supplementary" value=""/>
            </section>
            <section name="cov">
                <param name="methods" value="mean"/>
                <param name="trim_min" value="5"/>
                <param name="trim_max" value="95"/>
                <param name="min_covered_fraction" value="10"/>
                <param name="contig_end_exclusion" value="75"/>
            </section>
            <param name="output_format" value="dense"/>
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_text text="Contig"/>
                    <has_text text="Mean"/>
                    <has_text text="7seqs.fna"/>
                    <has_text text="genome1~random_sequence_length_11000"/>
                    <has_text text="genome2~seq1"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="mapped">
                <param name="mapped" value="not-mapped" />
                <conditional name="mode">
                    <param name="mode" value="co"/>
                    <conditional name="read_type">
                        <param name="type" value="single"/>
                        <param name="single" value="bad_reads.interleaved.fq"/>
                    </conditional>