Mercurial > repos > kpbioteam > ewastools

annotate minfi_read450k.xml @ 75:9c6fbb7d5a2a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
69
42c51d32e16c Uploaded
kpbioteam
parents: 5
diff changeset
1 <tool id="minfi_read450k" name="Minfi Read 450k" version="2.1.0">
75
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
2 <description>load .IDAT files</description>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
3 <requirements>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
4 <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
5
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
5 </requirements>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
7 #for $counter, $file in enumerate($files_red):
75
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
8 ln -s $file ./${counter+1}_Red.idat &&
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
9 #end for
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
10 #for $counter, $file in enumerate($files_grn):
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
11 ln -s $file ./${counter+1}_Grn.idat &&
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
12 #end for
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
13 Rscript '$read_idat_script'
5
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
14 ]]></command>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
15 <configfiles>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
16 <configfile name="read_idat_script"><![CDATA[
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
17 require("minfi", quietly = TRUE)
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
18 files<-list()
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
19 #for $counter, $input in enumerate($files_red):
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
20 files['${counter+1}'] <- '${counter+1}'
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
21 #end for
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
22 out <- read.metharray(files)
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
23 save(out, file = '$RGChannelSet')
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
24 ]]> </configfile>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
25 </configfiles>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
26 <inputs>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
27 <param type="data" name="files_red" multiple="true" format="idat" label="Red .IDAT files"/>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
28 <param type="data" name="files_grn" multiple="true" format="idat" label="Green .IDAT files" />
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
29 </inputs>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
30 <outputs>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
31 <data name="RGChannelSet" format="rdata" label="RGChannelSet"/>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
32 </outputs>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
33 <tests>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
34 <test>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
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"/>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
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"/>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
37 <output name="RGChannelSet" file="RGChannelSet.rdata"/>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
38 </test>
ab6e72fdf350 Uploaded
kpbioteam
parents:
diff changeset
39 </tests>
75
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
40 <help><![CDATA[
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
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.
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
42
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
43 ]]></help>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
44 <citations>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
45 <citation type="doi">10.18129/B9.bioc.illuminaio</citation>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
46 </citations>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
47 </tool>
9c6fbb7d5a2a planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents: 69
diff changeset
48