Mercurial > repos > kpbioteam > ewastools
annotate minfi_qc.xml @ 75:9c6fbb7d5a2a draft
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 | a1320b7a6d52 |
| children |
| rev | line source |
|---|---|
| 68 | 1 <tool id="minfi_qc" name="Minfi QC" version="@MINFI_VERSION@"> |
| 6 | 2 <description>provides a simple quality control matrix and plot</description> |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"> | |
| 8 <![CDATA[ | |
| 9 Rscript '$read_qc_script' | |
| 10 ]]> | |
| 11 </command> | |
| 12 <configfiles> | |
|
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
68
diff
changeset
|
13 <configfile name="read_qc_script"> |
| 6 | 14 <![CDATA[ |
| 15 require("minfi", quietly = TRUE) | |
| 16 | |
| 17 MSet <- get(load('$MethylSet')) | |
| 18 | |
| 19 qc <- getQC(MSet) | |
| 20 | |
| 21 write.table(qc, '$qctab') | |
| 22 | |
| 23 png('$qcpng') | |
| 24 plotQC(qc) | |
| 25 dev.off() | |
| 26 ]]> | |
|
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
68
diff
changeset
|
27 </configfile> |
|
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
68
diff
changeset
|
28 </configfiles> |
| 6 | 29 <inputs> |
|
75
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
68
diff
changeset
|
30 <param type="data" name="MethylSet" format="rdata" label="MethylSet" |
|
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
68
diff
changeset
|
31 help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/> |
| 6 | 32 </inputs> |
| 33 <outputs> | |
| 34 <data name="qctab" format="txt" label="Quality Control Report"/> | |
| 35 <data name="qcpng" format="png" label="Quality Control Plot"/> | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="MethylSet" value="MethylSet.rdata"/> | |
| 40 <output name="qctab" file="Quality_Control_Report.txt"/> | |
| 41 <output name="qcpng" file="Quality_Control_Plot.png" compare="sim_size"/> | |
| 42 </test> | |
| 43 </tests> | |
| 44 <help><![CDATA[ | |
| 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. | |
| 46 ]]></help> | |
| 47 <expand macro="citations" /> | |
| 48 </tool> |