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comparison minfi_read450k.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 42c51d32e16c
children fef50103f6b3
comparison
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74:53aaf097238c 75:9c6fbb7d5a2a
1 <tool id="minfi_read450k" name="Minfi Read 450k" version="2.1.0"> 1 <tool id="minfi_read450k" name="Minfi Read 450k" version="2.1.0">
2 <description>load .IDAT files</description> 2 <description>load .IDAT files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.24.0">bioconductor-minfi</requirement> 4 <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #for $counter, $file in enumerate($files_red): 7 #for $counter, $file in enumerate($files_red):
8 ln -s $file ./${counter+1}_Red.idat && 8 ln -s $file ./${counter+1}_Red.idat &&
9 #end for 9 #end for
10 #for $counter, $file in enumerate($files_grn): 10 #for $counter, $file in enumerate($files_grn):
11 ln -s $file ./${counter+1}_Grn.idat && 11 ln -s $file ./${counter+1}_Grn.idat &&
12 #end for 12 #end for
13 Rscript '$read_idat_script' 13 Rscript '$read_idat_script'
14 ]]></command> 14 ]]></command>
15 <configfiles> 15 <configfiles>
16 <configfile name="read_idat_script"><![CDATA[ 16 <configfile name="read_idat_script"><![CDATA[
17 require("minfi", quietly = TRUE) 17 require("minfi", quietly = TRUE)
18 files<-list() 18 files<-list()
35 <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"/> 35 <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"/>
36 <param name="files_grn" value="GSM1588707_8795207119_R06C02_Grn.idat,GSM1588706_8795207135_R02C02_Grn.idat,SM1588705_8795207119_R05C02_Grn.idat,GSM1588704_8795207135_R01C02_Grn.idat" ftype="idat"/> 36 <param name="files_grn" value="GSM1588707_8795207119_R06C02_Grn.idat,GSM1588706_8795207135_R02C02_Grn.idat,SM1588705_8795207119_R05C02_Grn.idat,GSM1588704_8795207135_R01C02_Grn.idat" ftype="idat"/>
37 <output name="RGChannelSet" file="RGChannelSet.rdata"/> 37 <output name="RGChannelSet" file="RGChannelSet.rdata"/>
38 </test> 38 </test>
39 </tests> 39 </tests>
40 <help><![CDATA[ 40 <help><![CDATA[
41 The tool load 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.]]></help> 41 The tool load 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.
42 <citations> 42
43 <citation type="doi">10.18129/B9.bioc.illuminaio</citation> 43 ]]></help>
44 </citations> 44 <citations>
45 </tool> 45 <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
46 46 </citations>
47 </tool>
48