Mercurial > repos > kpbioteam > ewastools

annotate minfi_qc.xml @ 0:bb6c8d38fad1 draft default tip

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 945cecdba6528d35c6dfa866f785f182c5dd22ed
author kpbioteam
date Fri, 07 Jun 2019 14:14:49 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
1 <tool id="minfi_qc" name="Minfi QC" version="@MINFI_VERSION@">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
2 <description>provides a simple quality control matrix and plot</description>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
3 <macros>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
4 <import>macros.xml</import>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
5 </macros>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
6 <expand macro="requirements" />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
7 <command detect_errors="exit_code">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
8 <![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
9 Rscript '$read_qc_script'
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
10 ]]>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
11 </command>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
12 <configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
13 <configfile name="read_qc_script">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
14 <![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
15 require("minfi", quietly = TRUE)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
16
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
17 MSet <- get(load('$MethylSet'))
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
18
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
19 qc <- getQC(MSet)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
20
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
21 write.table(qc, '$qctab')
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
22
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
23 png('$qcpng')
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
24 plotQC(qc)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
25 dev.off()
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
26 ]]>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
27 </configfile>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
28 </configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
29 <inputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
30 <param type="data" name="MethylSet" format="rdata" label="MethylSet"
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
31 help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
32 </inputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
33 <outputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
34 <data name="qctab" format="txt" label="Quality Control Report"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
35 <data name="qcpng" format="png" label="Quality Control Plot"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
36 </outputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
37 <tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
38 <test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
39 <param name="MethylSet" value="MethylSet.rdata"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
40 <output name="qctab" file="Quality_Control_Report.txt"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
41 <output name="qcpng" file="Quality_Control_Plot.png" compare="sim_size"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
42 </test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
43 </tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
44 <help><![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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.
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
46 ]]></help>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
47 <expand macro="citations" />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
parents:
diff changeset
48 </tool>