Mercurial > repos > kpbioteam > ewastools

annotate minfi_read450k.xml @ 76:fef50103f6b3 draft

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planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
author kpbioteam
date Fri, 07 Jun 2019 08:57:26 -0400
parents 9c6fbb7d5a2a
children
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1 <tool id="minfi_read450k" name="Minfi Read 450k" version="2.1.0">
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2 <description>load .IDAT files</description>
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3 <requirements>
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4 <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #for $counter, $input in enumerate($files_red):
fef50103f6b3 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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8 #set $redname = str( getattr( $input, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
fef50103f6b3 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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9 ln -s $input ./${redname} &&
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10 #end for
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11 #for $counter, $input in enumerate($files_grn):
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12 #set $grnname = str( getattr( $input, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
fef50103f6b3 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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13 ln -s $input ./${grnname} &&
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14 #end for
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15 Rscript '$read_idat_script'
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16 ]]></command>
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17 <configfiles>
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18 <configfile name="read_idat_script"><![CDATA[
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19 require("minfi", quietly = TRUE)
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20 out <- read.metharray(list.files(pattern="_Red.idat"))
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21 save(out, file = '$RGChannelSet')
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22 ]]> </configfile>
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23 </configfiles>
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24 <inputs>
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25 <param type="data" name="files_red" multiple="true" format="idat" label="Red .IDAT files"/>
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26 <param type="data" name="files_grn" multiple="true" format="idat" label="Green .IDAT files" />
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27 </inputs>
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28 <outputs>
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29 <data name="RGChannelSet" format="rdata" label="RGChannelSet"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="files_red" value="GSM1588707_8795207119_R06C02_Red.idat,GSM1588706_8795207135_R02C02_Red.idat,GSM1588705_8795207119_R05C02_Red.idat,GSM1588704_8795207135_R01C02_Red.idat" ftype="idat"/>
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fef50103f6b3 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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34 <param name="files_grn" value="GSM1588707_8795207119_R06C02_Grn.idat,GSM1588706_8795207135_R02C02_Grn.idat,GSM1588705_8795207119_R05C02_Grn.idat,GSM1588704_8795207135_R01C02_Grn.idat" ftype="idat"/>
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35 <output name="RGChannelSet" file="RGChannelSet.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 The tool loads the binary 450K array “IDAT” raw files generated by the Illumina Scanner. In addition to the methylated and an unmethylated intensity values for each 450,000 CpG positions, IDAT file contains some extra info such as control probes.
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41 ]]></help>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
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42 <citations>
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43 <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
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44 </citations>
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45 </tool>
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