comparison tools/mira4/mira4_de_novo.xml @ 6:626d5cfd01aa draft

Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)

5:ffefb87bd414

<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.1">
    <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
    <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">

                <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>
    <outputs>
        <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />
        <data name="out_maf" format="mira" label="MIRA de novo assembly" />
        <data name="out_log" format="txt" label="MIRA de novo log" />
    </outputs>

##This bar goes into the manifest as a comment line
#------------------------------------------------------------------------------

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:

6:626d5cfd01aa

<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.1">
    <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
    <requirements>
        <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">

                <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>
                </param>
                <when value="paired">
                    <param name="placement" type="select" label="Pairing type (segment placing)">
                        <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>
                    </param>
                    <!-- min/max validation is done via the <code> tag -->
                    <param name="min_size" type="integer" optional="true" min="0" value=""
                           label="Minimum size of 'good' DNA templates in the library preparation"
                           help="Optional, but if used you must also supply a maximum value." /> 
                    <param name="max_size" type="integer" optional="true" min="0" value=""
                           label="Maximum size of 'good' DNA templates in the library preparation"
                           help="Optional, but if used you must also supply a minimum value." />
                    <param name="naming" type="select" label="Pair naming convention">
                        <option value="solexa">Solexa/Illumina (using '/1' and '/2' suffixes)</option>
                        <option value="FR">Forward/Reverse scheme (using '.f*' and '.r*' suffixes)</option>
                        <option value="tigr">TIGR scheme (using 'TF*' and 'TR*' suffixes)</option>
                        <option value="sanger">Sanger scheme (see notes)</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)" />
        <data name="out_maf" format="mira" label="MIRA de novo assembly" />
        <data name="out_log" format="txt" label="MIRA de novo log" />
    </outputs>

##This bar goes into the manifest as a comment line
#------------------------------------------------------------------------------

readgroup
technology = ${rg.technology}
##Record the segment placement (if any)
#if str($rg.segments.type) == "paired"
segmentplacement = ${rg.segments.placement}
segmentnaming = ${rg.segments.naming}
#if str($rg.segments.min_size) != "" or str($rg.segments.max_size) != ""
##If our min/max validation failed I trust MIRA to give an error message...
templatesize = $rg.segments.min_size $rg.segments.max_size
#end if
#end if
#if str($rg.segments.type) == "none"
segmentplacement = ?
#end if
##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.


**Notes on paired reads**

.. class:: warningmark

MIRA uses read naming conventions to identify paired read partners
(and does not care about their order in the input files). In most cases,
the Solexa/Illumina setting is fine. For Sanger capillary sequencing,
you may need to rename your reads to match one of the standard conventions
supported by MIRA. For Roche 454 or Ion Torrent the appropriate settings
depend on how the FASTQ file was produced:

* If using Roche's ``sffinfo`` or older versions of ``sff_extract``
  to convert SFF files to FASTQ, your reads will probably have the
  ``---> <---`` orientation and use the ``.f`` and ``.r``
  suffixes (FR naming).

* If using a recent version of ``sff_extract``, then the ``/1`` and ``/2``
  suffixes are used (Solexa/Illumina style naming) and the original
  ``2---> 1--->`` orientation is preserved.

The reason for this is the raw data for Roche 454 and Ion Torrent paired-end
libraries sequences a circularised fragment such that the raw data begins
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
have the orientation ``2---> 1--->``. However, in order to use the data
with traditional tools expecting Sanger capillary style ``---> <---``
orientation it was common to reverse complement one of the pair to mimic this.


**Citation**

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