Mercurial > repos > kpbioteam > ewastools

annotate minfi_mset.xml @ 75:9c6fbb7d5a2a draft

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planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
author kpbioteam
date Mon, 20 May 2019 07:14:26 -0400
parents 53aaf097238c
children
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53aaf097238c planemo upload commit b4d745c28290bce5c7653886d70a63b001aaab19-dirty
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1 <tool id="minfi_mset" name="Minfi Mset" version="@MINFI_VERSION@">
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2 <description>Create objects contains CpGs signals</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 Rscript '$minfi_mset_script'
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10 ]]>
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11 </command>
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12 <configfiles>
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13 <configfile name="minfi_mset_script"><![CDATA[
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14 require("minfi", quietly = TRUE)
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15
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16 RGSet <- get(load('$RGChannelSet'))
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18 MSet <- preprocessRaw(RGSet)
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20 save(MSet,file = '$MethylSet')
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21
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22 ]]>
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23 </configfile>
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9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
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24 </configfiles>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
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25 <inputs>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
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26 <param type="data" name="RGChannelSet" format="rdata" label="RGChannelSet"
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
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27 help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array."/>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
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28 </inputs>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
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29 <outputs>
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30 <data name="MethylSet" format="rdata" label="MethylSet" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="RGChannelSet" value="RGChannelSet.rdata"/>
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35 <output name="MethylSet" file="MethylSet.rdata"/>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 This tool is transforming a class representing raw (unprocessed) data from a two color micro array - RGChannelSet into a class holding preprocessed data for Illumina methylation microarrays, mapped to genomic location - MethylSet.
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40 ]]></help>
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41 <expand macro="citations" />
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42 </tool>