annotate minfi_mset.xml @ 53:5cab527307f9 draft

Uploaded
author kpbioteam
date Fri, 22 Feb 2019 11:12:57 -0500
parents 3511473319c2
children 53aaf097238c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
1 <tool id="minfi_mset" name="Minfi mset" version="@MINFI_VERSION@">
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
2 <description>Create objects contains CpGs signals</description>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
3 <macros>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
4 <import>macros.xml</import>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
5 </macros>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
6 <expand macro="requirements" />
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
7 <command detect_errors="exit_code">
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
8 <![CDATA[
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
9 Rscript '$minfi_mset_script'
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
10 ]]>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
11 </command>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
12 <configfiles>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
13 <configfile name="minfi_mset_script"><![CDATA[
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
14 require("minfi", quietly = TRUE)
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
15
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
16 RGSet <- get(load('$RGChannelSet'))
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
17
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
18 MSet <- preprocessRaw(RGSet)
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
19
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
20 save(MSet,file = '$MethylSet')
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
21
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
22 ]]>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
23 </configfile>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
24 </configfiles>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
25 <inputs>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
26 <param type="data" name="RGChannelSet" format="rdata" label="RGChannelSet" help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array."/>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
27 </inputs>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
28 <outputs>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
29 <data name="MethylSet" format="rdata" label="MethylSet" />
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
30 </outputs>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
31 <tests>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
32 <test>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
33 <param name="RGChannelSet" value="RGChannelSet.rdata"/>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
34 <output name="MethylSet" file="MethylSet.rdata"/>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
35 </test>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
36 </tests>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
37 <help><![CDATA[
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
38 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.
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
39 ]]></help>
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
40 <expand macro="citations" />
3511473319c2 Uploaded
kpbioteam
parents:
diff changeset
41 </tool>