Mercurial > repos > cropgeeks > ukseed
changeset 12:d06b46d2e03c draft
Uploaded
| author | cropgeeks |
|---|---|
| date | Fri, 20 Apr 2018 04:18:09 -0400 |
| parents | 34ca6b2b028c |
| children | 8c273315322b |
| files | ukseed_2.xml |
| diffstat | 1 files changed, 49 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ukseed_2.xml Fri Apr 20 04:18:09 2018 -0400 @@ -0,0 +1,49 @@ +<tool id="ukseed_2_dartseq" name="UK SeeD (#2) Dartseq Analysis" version="0.0.1"> + <description>run a dartseq analysis</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_1.R $input + && + 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"/> + </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> \ No newline at end of file