Mercurial > repos > testtool > get_gsm
changeset 7:3eb1073638d7 draft
Deleted selected files
| author | testtool |
|---|---|
| date | Mon, 06 Feb 2017 05:10:13 -0500 |
| parents | 6bcb498025c1 |
| children | 5e1d49abfc99 |
| files | getGSMdata.R getGSMdata.xml tool_dependencies.xml |
| diffstat | 3 files changed, 0 insertions(+), 63 deletions(-) [+] |
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--- 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) -
--- 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 @@ -<tool id="GSM" name="getGSMdata" version="1.16.2"> - <requirements> -<tool_dependency> - <package name="methyldata_1_16_2" version="1.16.2"> - <repository name="methyldata_1_16_2" owner="testtool" prior_installation_required="True" /> - </package> -</tool_dependency> -</requirements> -<stdio> - <exit_code range="1:" /> -</stdio> - <command> Rscript $__tool_directory__/getGSMdata.R "$GSE" "$GSMTable" </command> - <inputs> - <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> - </inputs> - <outputs> - <data format="txt" name="GSMTable" label="GSMTable.txt"/> - </outputs> - <tests> - <test> - <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSE" value="GSE51547"/> - </collection> - </element> - </param> - <output format="txt" name="GSMTable" label="test-data/GSMTable.txt"/> - </test> - </tests> - <help> -**Description** -</help> -<citations> -GEO -</citations> -</tool>
--- 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 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="methyldata_1_16_2" version="1.16.2"> - <repository changeset_revision="ea44a0861444" name="methyldata_1_16_2" owner="testtool" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>