changeset 0:fea57210de6c draft

Uploaded

Binary file findBlocks/._.DS_Store has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findBlocks/findBlocks.R	Sun Jun 11 08:53:04 2017 -0400
@@ -0,0 +1,22 @@
+require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
+require("minfi", quietly = TRUE)
+
+options(warn = -1)
+options("download.file.method"="wget")
+
+args <- commandArgs(trailingOnly = TRUE)
+
+input = args[1]
+output = args[2]
+
+GRset <- get(load(input))
+
+blocks <- blockFinder(GRset, design, coef = 2, what = c("Beta", "M"),
+            cluster = NULL, cutoff = NULL,
+            pickCutoff = FALSE, pickCutoffQ = 0.99,
+            nullMethod = c("permutation","bootstrap"),
+            smooth = TRUE, smoothFunction = locfitByCluster,
+            B = ncol(permutations), permutations = NULL,
+            verbose = TRUE)
+
+write.table(blocks, output)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findBlocks/findBlocks.xml	Sun Jun 11 08:53:04 2017 -0400
@@ -0,0 +1,38 @@
+<tool id="findBlocks" name="findBlocks" version="1.18.4">
+  <requirements>
+        <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
+    </requirements>
+<stdio>
+   <exit_code range="1:" />
+</stdio>
+  <command> Rscript $__tool_directory__/findBlocks.R "$input" "$output" </command>
+  <inputs>
+    <param name="input" format="RData"label="getGenomicRatioSet.RData" help="e.g. 'GSE51547'"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="findBlocks.txt"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+           <collection type="data">
+                <element format="RData" name="input" label="test-data/GenomicRatioSet.Rdata"/>
+          </collection>
+        </element>
+        </param>
+        <output format="txt" name="output" label="test-data/findBlocks.txt"/>
+        </test>
+    </tests>
+  <help>
+**What it does**
+Finds blocks (large scale regions) of methylation differences for Illumina methylation arrays.
+**Input**
+GenomicRatioSet object e.g. output from getGRsetFromGEO tool
+**Output**
+Text file
+</help>
+<citations>
+<citation type="doi">10.1093/bioinformatics/btu049</citation>
+</citations>
+</tool>