annotate minfi_qc.xml @ 55:ca52f81202eb draft

Uploaded
author kpbioteam
date Fri, 22 Feb 2019 11:13:39 -0500
parents 4f34e3f73ebf
children a1320b7a6d52
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
1 <tool id="minfi_qc" name="Minfi qc" version="@MINFI_VERSION@">
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
2 <description>provides a simple quality control matrix and plot</description>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
3 <macros>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
4 <import>macros.xml</import>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
5 </macros>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
6 <expand macro="requirements" />
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
7 <command detect_errors="exit_code">
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
8 <![CDATA[
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
9 Rscript '$read_qc_script'
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
10 ]]>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
11 </command>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
12 <configfiles>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
13 <configfile name="read_qc_script">
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
14 <![CDATA[
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
15 require("minfi", quietly = TRUE)
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
16
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
17 MSet <- get(load('$MethylSet'))
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
18
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
19 qc <- getQC(MSet)
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
20
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
21 write.table(qc, '$qctab')
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
22
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
23 png('$qcpng')
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
24 plotQC(qc)
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
25 dev.off()
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
26 ]]>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
27 </configfile>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
28 </configfiles>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
29 <inputs>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
30 <param type="data" name="MethylSet" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
31 location."/>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
32 </inputs>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
33 <outputs>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
34 <data name="qctab" format="txt" label="Quality Control Report"/>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
35 <data name="qcpng" format="png" label="Quality Control Plot"/>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
36 </outputs>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
37 <tests>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
38 <test>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
39 <param name="MethylSet" value="MethylSet.rdata"/>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
40 <output name="qctab" file="Quality_Control_Report.txt"/>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
41 <output name="qcpng" file="Quality_Control_Plot.png" compare="sim_size"/>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
42 </test>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
43 </tests>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
44 <help><![CDATA[
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
45 Quality Control (QC) outputs plot of the log median intensity in both the methylated (M) and unmethylated (U) channels. When plotting these two medians against each other the good samples cluster together, while failed samples tend to separate and have lower median intensities.
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
46 ]]></help>
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
47 <expand macro="citations" />
4f34e3f73ebf Uploaded
kpbioteam
parents:
diff changeset
48 </tool>