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annotate minfi_rset.xml @ 0:bb6c8d38fad1 draft default tip

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planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
author kpbioteam
date Fri, 07 Jun 2019 14:14:49 -0400
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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1 <tool id="minfi_rset" name="Minfi Rset" version="@MINFI_VERSION@">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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2 <description>store Beta values and/or M values</description>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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3 <macros>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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4 <import>macros.xml</import>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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5 </macros>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
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6 <expand macro="requirements" />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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7 <command detect_errors="exit_code">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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8 <![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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9 Rscript '$read_rset_script'
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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10 ]]>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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11 </command>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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12 <configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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13 <configfile name="read_rset_script">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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14 <![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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15 require("minfi", quietly = TRUE)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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16 MSet <- get(load('$mset'))
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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17
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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18 RSet <- ratioConvert(MSet, what = "both", keepCN = TRUE)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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19
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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20 save(RSet,file = '$rset')
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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21 ]]> </configfile>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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22 </configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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23 <inputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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24 <param type="data" name="mset" format="rdata" label="MethylSet"
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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25 help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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26 </inputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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27 <outputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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28 <data name="rset" format="rdata" label="RatioSet"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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29 </outputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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30 <tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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31 <test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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32 <param name="mset" value="MethylSet.rdata"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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33 <output name="rset" file="RatioSet.rdata"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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34 </test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
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35 </tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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36 <help><![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
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37 RSet class holds preprocessed data for Illumina methylation microarrays. It contains respectively the Beta value matrix, M value matrix and the Copy Number matrix.
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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38 ]]></help>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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39 <expand macro="citations" />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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40 </tool>