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1 <tool id="ukseed_stage_1" name="UK SeeD Dartseq Analysis #1" version="0.0.2">
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2 <description>run a dartseq analysis (stage #1)</description>
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3 <requirements>
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4 <requirement type="package" version="1.12.2">bioconductor-snprelate</requirement>
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5 <requirement type="package" version="1.90b4">plink</requirement>
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6 <requirement type="package" version="0.8_14">r-amap</requirement>
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7 <requirement type="package" version="1.0">r-dartr</requirement>
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8 <requirement type="package" version="1.8_0">r-labdsv</requirement>
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9 <!--<requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>-->
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10 </requirements>
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11
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12 <command><![CDATA[
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13 Rscript --vanilla $__tool_directory__/dartseq_seeduk_1.R $input > $output
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14 ]]></command>
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16 <inputs>
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17 <param format="csv,txt" name="input" type="data" label="Input file"
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18 help="Input file of genotype data"/>
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19 </inputs>
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20
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21 <outputs>
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22 <data name="output" format="txt" />
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23 </outputs>
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24
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25 <stdio>
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26 <exit_code range="1:" />
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27 </stdio>
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28
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29 <help>
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27
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30 This pipeline has been developed for loading a DArT SNP or SilicoDArT, report and apply filters to those datasets based on locus and
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31 individuals call rates and locus reproducibility. It also allows data export for other formats such as GDS, plink bed and a text file
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32 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
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33 pipeline perform a Principal Coordinates Analysis (PCoA, = Multidimensional scaling, MDS) to explore similarities of data and outputs
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34 a vcf file suitable for visualizing in CurlyWhirly.
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35
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36 In **UK-SeeD Data Analysis Infrastructure**, a BBSRC-Newton funded project, we have deployed an advanced computing hardware and software
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37 platform for the analysis of large genomics datasets for wheat varieties. The platform integrates computing resources and bioinformatics
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38 expertise to enable crop geneticists to implement sophisticated data analysis algorithms to improve the use of genetic resources for
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39 wheat and other important crops. The computing platform is distributed across the partners’ sites with hardware deployed at CIMMYT
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40 (Mexico) and the Earlham Institute (UK).
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41
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42 |LOGOS|
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43
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44 .. |LOGOS| image:: https://ics.hutton.ac.uk/resources/ukseed/logos.png
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45 </help>
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46
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47 <citations>
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48 </citations>
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49 </tool> |
