Mercurial > repos > testtool > get_gsm

changeset 7:3eb1073638d7 draft

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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(-) [+]
line wrap: on
line diff
--- 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>