view ukseed_stage1.xml @ 27:558a46a635a9 draft

Uploaded

<tool id="ukseed_stage_1" name="UK SeeD Dartseq Analysis #1" version="0.0.2">
    <description>run a dartseq analysis (stage #1)</description>
    <requirements>
        <requirement type="package" version="1.12.2">bioconductor-snprelate</requirement>
		<requirement type="package" version="1.90b4">plink</requirement>
		<requirement type="package" version="0.8_14">r-amap</requirement>
		<requirement type="package" version="1.0">r-dartr</requirement>
		<requirement type="package" version="1.8_0">r-labdsv</requirement>
		<!--<requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>-->
    </requirements>

    <command><![CDATA[
	    Rscript --vanilla $__tool_directory__/dartseq_seeduk_1.R $input > $output
    ]]></command>
	
    <inputs>
        <param format="csv,txt" name="input" type="data" label="Input file"
            help="Input file of genotype data"/>
    </inputs>

    <outputs>
        <data name="output" format="txt" />
    </outputs>
  
    <stdio>
        <exit_code range="1:" />
    </stdio>

<help>
This pipeline has been developed for loading a DArT SNP or SilicoDArT, report and apply filters to those datasets based on locus and
individuals call rates and locus reproducibility. It also allows data export for other formats such as GDS, plink bed and a text file
with a header line, and then one line per sample with V+6 where V is the number of variants suitable for loading into R. Finally the
pipeline perform a Principal Coordinates Analysis (PCoA, = Multidimensional scaling, MDS) to explore similarities of data and outputs
a vcf file suitable for visualizing in CurlyWhirly.

In **UK-SeeD Data Analysis Infrastructure**, a BBSRC-Newton funded project, we have deployed an advanced computing hardware and software
platform for the analysis of large genomics datasets for wheat varieties. The platform integrates computing resources and bioinformatics
expertise to enable crop geneticists to implement sophisticated data analysis algorithms to improve the use of genetic resources for
wheat and other important crops. The computing platform is distributed across the partners’ sites with hardware deployed at CIMMYT
(Mexico) and the Earlham Institute (UK).  

|LOGOS|

.. |LOGOS| image:: https://ics.hutton.ac.uk/resources/ukseed/logos.png
</help>

    <citations>
    </citations>
</tool>