comparison tools/mira4/mira4_de_novo.xml @ 15:b0ffe0e7282b draft

Uploaded v0.0.2 preview 7, fixed bash syntax error

14:133b863a8a40

                <option value="454">Roche 454</option>
                <option value="iontor">Ion Torrent</option>
                <option value="pcbiolq">PacBio low quality (raw)</option>
                <option value="pcbiohq">PacBio high quality (corrected)</option>
                <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
		<!-- TODO reference/backbone as an entry here? -->
            </param>
            <conditional name="segments">
                <param name="type" type="select" label="Are these paired reads?">
                    <option value="paired">Paired reads</option>
                    <option value="none">Single reads or not relevant (e.g. primer walking with Sanger capillary sequencing)</option>

                        <option value="stlouis">St. Louis scheme (see notes)</option>
                    </param>
                </when>
                <when value="none" /><!-- no further questions -->
            </conditional>
	    <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
		   help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
        </repeat>
    </inputs>
    <code file="mira4_validator.py" />
    <outputs>
        <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />

            <param name="type" value="none" />
            <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
            <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
        </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" />

15:b0ffe0e7282b

                <option value="454">Roche 454</option>
                <option value="iontor">Ion Torrent</option>
                <option value="pcbiolq">PacBio low quality (raw)</option>
                <option value="pcbiohq">PacBio high quality (corrected)</option>
                <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
                <!-- TODO reference/backbone as an entry here? -->
            </param>
            <conditional name="segments">
                <param name="type" type="select" label="Are these paired reads?">
                    <option value="paired">Paired reads</option>
                    <option value="none">Single reads or not relevant (e.g. primer walking with Sanger capillary sequencing)</option>

                        <option value="stlouis">St. Louis scheme (see notes)</option>
                    </param>
                </when>
                <when value="none" /><!-- no further questions -->
            </conditional>
            <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
                  help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
        </repeat>
    </inputs>
    <code file="mira4_validator.py" />
    <outputs>
        <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />

            <param name="type" value="none" />
            <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
            <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
        </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" />