comparison tools/mira_3_4/mira.xml @ 9:b1d60b46d282 draft

Uploaded v0.0.8 take 3, citation information added, commented out test

8:da604cc07658

        <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
        <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
        <data name="out_log" format="txt" label="MIRA log" />
    </outputs>
    <tests>
        <test>
            <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
                 strain data and miraSearchESTSNPs. Here we just assemble it. --> 
            <param name="job_method" value="denovo" />
            <param name="job_type" value="est" />
            <param name="job_qual" value="accurate" />
            <param name="condBackbone.use" value="false" />
            <param name="condSanger.use" value="true" />

            <param name="condRoche.use" value="false" />
            <param name="condIllumina.use" value="false" /> 
            <param name="condIonTorrent.use" value="false" />
            <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
	</test>
    </tests>
    <help>

**What it does**

Runs MIRA v3.4, collects the output, and throws away all the temporary files.

**Citation**

If you use this tool in scientific work leading to a publication, please cite:

Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 

    </help>
</tool>

9:b1d60b46d282

        <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
        <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
        <data name="out_log" format="txt" label="MIRA log" />
    </outputs>
    <tests>
            <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
                 strain data and miraSearchESTSNPs. Here we just assemble it. --> 
<!--
Commenting out test until Galaxy framework is fixed,
https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
        <test>
            <param name="job_method" value="denovo" />
            <param name="job_type" value="est" />
            <param name="job_qual" value="accurate" />
            <param name="condBackbone.use" value="false" />
            <param name="condSanger.use" value="true" />

            <param name="condRoche.use" value="false" />
            <param name="condIllumina.use" value="false" /> 
            <param name="condIonTorrent.use" value="false" />
            <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
	</test>
-->
    </tests>
    <help>

**What it does**

Runs MIRA v3.4, collects the output, and throws away all the temporary files.

MIRA is an open source assembly tool capable of handling sequence data from
a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
Ion Torrent).

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:

Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
http://dx.doi.org/10.7717/peerj.167

Chevreux et al. (1999).
Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 

    </help>
</tool>