# HG changeset patch
# User testtool
# Date 1486375813 18000
# Node ID 3eb1073638d7c26d8ac8d463d1e4c49dccb12205
# Parent 6bcb498025c118d309f51f2abe846854e415eaec
Deleted selected files
diff -r 6bcb498025c1 -r 3eb1073638d7 getGSMdata.R
--- a/getGSMdata.R Mon Feb 06 05:09:40 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-require("rentrez", quietly = TRUE)
-
-args <- commandArgs(trailingOnly = TRUE)
-GSE = args[1]
-GSMTable = args[2]
-
-search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
-
-rec2 <- entrez_summary(db = "gds",
- id = search1$ids,
- version = "2.0")
-
-extract <- extract_from_esummary(rec2,rownames(summary(rec2)))
-
-samples <- extract$samples
-colnames(samples)[which(names(samples) == "accession")] <- "ID"
-colnames(samples)[which(names(samples) == "title")] <- "Phenotype"
-
-write.table(samples, GSMTable, row.names = FALSE, sep = "\t",quote = FALSE)
-
diff -r 6bcb498025c1 -r 3eb1073638d7 getGSMdata.xml
--- a/getGSMdata.xml Mon Feb 06 05:09:40 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
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- Rscript $__tool_directory__/getGSMdata.R "$GSE" "$GSMTable"
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-**Description**
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-GEO
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diff -r 6bcb498025c1 -r 3eb1073638d7 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Feb 06 05:09:40 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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