annotate minfi_getm.xml @ 60:b0b694934751 draft

Uploaded
author kpbioteam
date Fri, 22 Feb 2019 11:17:35 -0500
parents 1e048d0cda1d
children 20e5954f9dc2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
1 <tool id="minfi_getM" name="minfi Get M" version="@MINFI_VERSION@">
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
2 <description>returns the Fisher information corresponding to a model and a design</description>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
3 <macros>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
4 <import>macros.xml</import>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
5 </macros>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
6 <expand macro="requirements" />
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
7 <command detect_errors="exit_code">
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
8 <![CDATA[
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
9 Rscript '$minfi_m_script'
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
10 ]]>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
11 </command>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
12 <configfiles>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
13 <configfile name="minfi_m_script"><![CDATA[
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
14 require("minfi", quietly = TRUE)
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
15 MSet <- get(load('$mset'))
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
16
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
17 m <- getM(MSet)
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
18
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
19 write.table(m, '$matrix')
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
20 ]]>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
21 </configfile>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
22 </configfiles>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
23 <inputs>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
24 <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
25 location."/>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
26 </inputs>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
27 <outputs>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
28 <data name="matrix" format="txt" label="M Value Matrix"/>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
29 </outputs>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
30 <tests>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
31 <test>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
32 <param name="mset" value="MethylSet.rdata"/>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
33 <output name="matrix" file="M_Value_Matrix.txt"/>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
34 </test>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
35 </tests>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
36 <help><![CDATA[
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
37 This tool output M value the logit representation of methylation level ratio based on intensities between methylated and unmethylated alleles in each probed CpG site.
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
38 ]]></help>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
39 <expand macro="citations" />
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
40 </tool>
1e048d0cda1d Uploaded
kpbioteam
parents:
diff changeset
41