view ukseed_stage2.xml @ 17:86b97a659d72 draft

Uploaded

<tool id="ukseed_dartseq_2" name="UK SeeD Dartseq Analysis #2" version="0.0.1">
    <description>run a dartseq analysis (stage #2)</description>
    <requirements>
        <!--
		<requirement type="package" version="1.90b4">plink</requirement>
		<requirement type="package" version="1.12.2">bioconductor-snprelate</requirement>
		<requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
		<requirement type="package" version="0.8_14">r-amap</requirement>
		<requirement type="package" version="1.2_16">r-rgdal</requirement>
		<requirement type="package" version="1.0">r-dartr</requirement>
		-->
    </requirements>

    <command><![CDATA[
	    Rscript --vanilla $__tool_directory__/dartseq_seeduk_1c.R $input $gl_call_rate $gl_rep $gl_final
		&&		
		plink --bfile test --recode A 
		&&		
		Rscript --vanilla $__tool_directory__/dartseq_seeduk_2.R $output		
    ]]></command>
	
    <inputs>
        <param format="csv" name="input" type="data" label="Input file"
            help="Input file of genotype data"/>
		
		<param name="gl_call_rate" type="float" value="0.75"
			label="gl_call_rate"
			help="gl_call_rate"/>
			
		<param name="gl_final" type="float" value="0.8"
			label="gl_final"
			help="gl_final"/>
			
		<param name="gl_rep" type="float" value="0.98"
			label="gl_rep"
			help="gl_rep"/>
    </inputs>

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

<help>
In ``UK SeeD``, 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).  

|JHI|

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

    <citations>
    </citations>
</tool>