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annotate minfi_mset.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_mset" name="Minfi Mset" version="@MINFI_VERSION@">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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2 <description>Create objects contains CpGs signals</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
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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 '$minfi_mset_script'
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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10 ]]>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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11 </command>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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12 <configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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13 <configfile name="minfi_mset_script"><![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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14 require("minfi", quietly = TRUE)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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16 RGSet <- get(load('$RGChannelSet'))
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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18 MSet <- preprocessRaw(RGSet)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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20 save(MSet,file = '$MethylSet')
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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22 ]]>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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23 </configfile>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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24 </configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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25 <inputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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26 <param type="data" name="RGChannelSet" format="rdata" label="RGChannelSet"
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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27 help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array."/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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28 </inputs>
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 <data name="MethylSet" format="rdata" label="MethylSet" />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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31 </outputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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32 <tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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33 <test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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34 <param name="RGChannelSet" value="RGChannelSet.rdata"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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35 <output name="MethylSet" file="MethylSet.rdata"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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36 </test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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37 </tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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38 <help><![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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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.
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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40 ]]></help>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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41 <expand macro="citations" />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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42 </tool>