Mercurial > repos > kpbioteam > minfi_qc

changeset 0:7bd0d3c7a8d3 draft

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planemo upload
author kpbioteam
date Tue, 06 Feb 2018 05:40:33 -0500
parents
children 88f94d4c59c4
files MSet.rdata minfi_qc.R minfi_qc.xml qc.png qc.txt test-data/MSet.rdata test-data/qc.png test-data/qc.txt
diffstat 8 files changed, 60 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
Binary file MSet.rdata has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_qc.R	Tue Feb 06 05:40:33 2018 -0500
@@ -0,0 +1,17 @@
+require("minfi", quietly = TRUE)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+input = args[1] 
+output1 = args[2]
+output2 = args[3]
+
+MSet <- get(load(input))
+
+qc <- getQC(MSet)
+
+write.table(qc, output1)
+
+png(output2)
+plotQC(qc)
+dev.off()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_qc.xml	Tue Feb 06 05:40:33 2018 -0500
@@ -0,0 +1,29 @@
+<tool id="minfi_qc" name="minfi_qc" version="0.1.0">
+    <description>provides a simple quality control matrix and plot</description>
+    <requirements>
+        <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript  ${__tool_directory__}/minfi_qc.R  "$input1" "$output1" "$output2"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="rdata" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="txt" />
+        <data name="output2" format="png" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="MSet.rdata"/>
+            <output name="output1" file="qc.txt"/>
+            <output name="output2" file="qc.png"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Estimate sample-specific quality control (QC) for methylation data
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu049</citation>
+    </citations>
+</tool>
\ No newline at end of file
Binary file qc.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qc.txt	Tue Feb 06 05:40:33 2018 -0500
@@ -0,0 +1,7 @@
+"mMed" "uMed"
+"5723646052_R02C02" 11.695663296788 11.8205778826558
+"5723646052_R04C01" 11.9904585650737 11.9527412471865
+"5723646052_R05C02" 11.5560269927247 12.0539258815311
+"5723646053_R04C02" 12.0660891904578 12.0927571409199
+"5723646053_R05C02" 12.2333200827308 12.0844762374539
+"5723646053_R06C02" 11.3685064615077 11.6059424396254
Binary file test-data/MSet.rdata has changed
Binary file test-data/qc.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/qc.txt	Tue Feb 06 05:40:33 2018 -0500
@@ -0,0 +1,7 @@
+"mMed" "uMed"
+"5723646052_R02C02" 11.695663296788 11.8205778826558
+"5723646052_R04C01" 11.9904585650737 11.9527412471865
+"5723646052_R05C02" 11.5560269927247 12.0539258815311
+"5723646053_R04C02" 12.0660891904578 12.0927571409199
+"5723646053_R05C02" 12.2333200827308 12.0844762374539
+"5723646053_R06C02" 11.3685064615077 11.6059424396254