comparison tools/mira4/mira4_de_novo.xml @ 5:ffefb87bd414 draft

Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)

4:df86ed992a1b

    <requirements>
        <requirement type="python-module">Bio</requirement>
        <requirement type="binary">mira</requirement>
        <requirement type="package" version="4.0">MIRA</requirement>
    </requirements>
    <version_command interpreter="python">mira4.py -v</version_command>
    <command interpreter="python">
mira4.py $manifest $out_maf $out_fasta $out_log
    </command>
    <inputs>
        <param name="job_type" type="select" label="Assembly type">

                <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>
	    <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>

readgroup
technology = ${rg.technology}
##MIRA will accept multiple filenames on one data line, or multiple data lines
#for $f in $rg.filenames
##Must now map Galaxy datatypes to MIRA file types...
#if $f.ext.startswith("fastq")
##MIRA doesn't like fastqsanger etc, just plain old fastq:
data = fastq::$f
#elif $f.ext == "mira"

a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent
and also PacBio).

It is particularly suited to small genomes such as bacteria.

**Citation**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

5:ffefb87bd414

    <requirements>
        <requirement type="python-module">Bio</requirement>
        <requirement type="binary">mira</requirement>
        <requirement type="package" version="4.0">MIRA</requirement>
    </requirements>
    <version_command interpreter="python">mira4.py --version</version_command>
    <command interpreter="python">
mira4.py $manifest $out_maf $out_fasta $out_log
    </command>
    <inputs>
        <param name="job_type" type="select" label="Assembly type">

                <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>
            <param name="segment_placement" type="select" label="Pairing type (segment placing)">
                <option value="">None (e.g. single end sequencing)</option>
                <option value="FR">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
                <option value="RF">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
                <option value="SB">2---&gt; 1---&gt; (e.g. Roche 454 paired-end libraries or IonTorrent long-mate; see note)</option>
                <option value="?">Unknown or not relevant (e.g. primer walking with Sanger capillary sequencing)</option>
            </param>
	    <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>

readgroup
technology = ${rg.technology}
##MIRA will accept multiple filenames on one data line, or multiple data lines
#for $f in $rg.filenames
#if str($rg.segment_placement) != ""
##Record the segment placement (if any)
segmentplacement = ${rg.segment_placement}
#end if
##Must now map Galaxy datatypes to MIRA file types...
#if $f.ext.startswith("fastq")
##MIRA doesn't like fastqsanger etc, just plain old fastq:
data = fastq::$f
#elif $f.ext == "mira"

a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent
and also PacBio).

It is particularly suited to small genomes such as bacteria.

**Notes**

.. class:: warningmark

Note that the raw data for Roche 454 and Ion Torrent paired-end libraries
sequences a circularised fragment such that the raw data starts with the
end of the fragment, a linker, then the start of the fragment. This means
both the start and end are sequenced from the same strand, and thus should
be given to MIRA as orientation "2---> 1--->". However, in order to
use this data with traditional tools expecting Sanger capillary style
libraries which expect "---> <---" your FASTQ files may have been
pre-processed to mimic this by reverse complementing one of the pair.

**Citation**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers: