comparison tools/mira4/mira4_de_novo.xml @ 21:4abe8d59a438 draft

Uploaded v0.0.4 preview 1; fix getting BAM without MAF

20:aeb3e35f8236

            <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
            <param name="maf_wanted" value="true"/>
            <param name="bam_wanted" value="true"/>
            <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
            <output name="out_bam" file="empty_file.dat" compare="contains" />
            <output name="out_maf" file="empty_file.dat" compare="contains" />
            <output name="out_log" file="empty_file.dat" compare="contains" />
        </test>
        <!-- Simple assembly based on MIRA's minidemo/solexa1 example
             Note we're using just one repeat group,
             but two parameters within the repeat (filename, no pairing)

        <test>
            <param name="job_type" value="genome" />
            <param name="job_quality" value="accurate" />
            <param name="type" value="none" />
            <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
            <param name="maf_wanted" value="true"/>
            <param name="bam_wanted" value="true"/>
            <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
            <output name="out_bam" file="empty_file.dat" compare="contains" />
            <output name="out_maf" file="empty_file.dat" compare="contains" />
            <output name="out_log" file="empty_file.dat" compare="contains" />
        </test>
    </tests>
    <help>

21:4abe8d59a438

            <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
            <param name="maf_wanted" value="true"/>
            <param name="bam_wanted" value="true"/>
            <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
            <output name="out_bam" file="empty_file.dat" compare="contains" />
            <!-- TODO: Suggest startswith as a compare method? -->
            <output name="out_maf" file="header.mira" compare="contains" />
            <output name="out_log" file="empty_file.dat" compare="contains" />
        </test>
        <!-- Simple assembly based on MIRA's minidemo/solexa1 example
             Note we're using just one repeat group,
             but two parameters within the repeat (filename, no pairing)

        <test>
            <param name="job_type" value="genome" />
            <param name="job_quality" value="accurate" />
            <param name="type" value="none" />
            <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
            <param name="maf_wanted" value="false"/>
            <param name="bam_wanted" value="false"/>
            <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
            <output name="out_log" file="empty_file.dat" compare="contains" />
        </test>
    </tests>
    <help>