changeset 10:cbc8174bd361 draft

Uploaded
author testtool
date Mon, 20 Mar 2017 06:54:27 -0400
parents 19ea355e26b3
children 983651783ce9
files GEO/.Rhistory GEO/._.DS_Store GEO/getGEO.R GEO/getGEO.xml GEO/test-data/._.DS_Store GEO/test-data/._input.csv GEO/test-data/IlmnTable.txt GEO/test-data/MetaTable.txt GEO/test-data/gmTable.txt GEO/test-data/input.csv GEO/tool_dependencies.xml getGEO/.Rhistory getGEO/._.DS_Store getGEO/getGEO.R getGEO/getGEO.xml getGEO/test-data/._.DS_Store getGEO/test-data/._input.csv getGEO/test-data/IlmnTable.txt getGEO/test-data/MetaTable.txt getGEO/test-data/gmTable.txt getGEO/test-data/input.csv getGEO/tool_dependencies.xml
diffstat 22 files changed, 971535 insertions(+), 971535 deletions(-) [+]
line wrap: on
line diff
--- a/GEO/.Rhistory	Tue Feb 28 05:11:54 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-??options
-options(warn = -1)
-+options("download.file.method"="wget")
-options("download.file.method"="wget")
-options(warn = -1,"download.file.method"="wget")
-??getPlatform
-??getPlatform
Binary file GEO/._.DS_Store has changed
--- a/GEO/getGEO.R	Tue Feb 28 05:11:54 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-require("BiocGenerics", quietly = TRUE)
-require("data.table", quietly = TRUE)
-require("GEOquery", quietly = TRUE)
-require("rtracklayer", quietly = TRUE)
-require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
-
-options("download.file.method.GEOquery"="wget")
-options(warn = -1)
-
-args <- commandArgs(trailingOnly = TRUE)
-GSMTable = args[1]
-protocol = args[2]
-platform = args[3]
-Data_Table = args[4]
-
-TAB = fread(GSMTable)
-
-if (is.null(TAB)) {
-  stop("Must specify input files")
-} else {
-  GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
-  IlmnIDTable <- Table(GEODataTable)
-  MetaData <- data.frame(Meta(GEODataTable))
-
-
-  write.table(MetaData, protocol, row.names = FALSE, sep = "\t")
-}
-
-hm450.hg19 <- getPlatform()
-
-IlmnInfo <-
-  data.table(
-    IlmnID = names(hm450.hg19),
-    CHR = as.data.frame(hm450.hg19@seqnames)$value,
-    BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
-  )
-
-
-write.table(IlmnInfo, platform, row.names = FALSE, sep = "\t")
-
-
-if (length(TAB$ID) > 1) {
-  mysamples <-
-    do.call("data.table", lapply(TAB$ID[-1], function(x)
-      Table(getGEO(x, getGPL = FALSE))[, -1]))
-
-  gmSet <- data.table(IlmnIDTable[, -1], mysamples)
-
-} else {
-  gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
-}
-
-write.table(gmSet, Data_Table, row.names = FALSE,quote=FALSE,sep="\t")
-
--- a/GEO/getGEO.xml	Tue Feb 28 05:11:54 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<tool id="GEO" name="getGEO" version="1.16.2">
-  <requirements>
-         <requirement type="package" version="3.2.1">R</requirement>
-     </requirements>
-<stdio>
-    <exit_code range="1:" />
- </stdio>
-  <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$protocol" "$platform" "$Data_Table"</command>
-  <inputs>
-    <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
-      <validator type="empty_field" message="This field is required."/>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="txt" name="protocol" label="protocol.txt"/>
-    <data format="txt" name="platform" label="platform.txt"/>
-    <data format="txt" name="Data_Table" label="Data_Table.txt"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="test">
-      <element name="test-data">
-          <collection type="data">
-              <element name="GSMTable" value="test-data/input.csv" />
-          </collection>
-        </element>
-        </param>
-        <output format="txt" name="protocol" label="test-data/protocol.txt"/>
-        <output format="txt" name="platform" label="test-data/platform.txt"/>
-        <output format="txt" name="Data_Table" label="test-data/Data_Table.txt"/>
-        </test>
-    </tests>
-  <help>
-**Description**
-</help>
-<citations>
-GEO
-</citations>
-</tool>
Binary file GEO/test-data/._.DS_Store has changed
Binary file GEO/test-data/._input.csv has changed
--- a/GEO/test-data/IlmnTable.txt	Tue Feb 28 05:11:54 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,485578 +0,0 @@
-"IlmnID","CHR","BP"
-"cg04913815","chr16",60438
-"cg01686861","chr16",60700
-"cg05558259","chr16",61037
-"cg26978960","chr16",62412
-"cg03792876","chr16",73195
-"cg09699726","chr16",91554
-"cg07549526","chr16",91663
-"cg02851049","chr16",101212
-"cg11876012","chr16",101638
-"cg14820573","chr16",102073
-"cg14747225","chr16",102976
-"cg16670573","chr16",103375
-"cg09499248","chr16",103483
-"cg00762468","chr16",103568
-"cg05055400","chr16",103592
-"cg09969830","chr16",103646
-"cg00958578","chr16",103715
-"cg11653271","chr16",103723
-"cg01188584","chr16",103853
-"cg03974483","chr16",103985
-"cg08718695","chr16",104135
-"cg01062126","chr16",104539
-"cg00992207","chr16",107404
-"cg00914902","chr16",108066
-"cg27248189","chr16",110257
-"cg06194960","chr16",111362
-"cg07608562","chr16",111610
-"cg20220196","chr16",111753
-"cg09201525","chr16",111823
-"cg03333116","chr16",112396
-"cg04721268","chr16",112802
-"cg01403103","chr16",112804
-"cg01502407","chr16",113107
-"cg04322210","chr16",114987
-"cg26933686","chr16",115957
-"cg00179196","chr16",117934
-"cg07405083","chr16",119384
-"cg06934747","chr16",120902
-"cg00525011","chr16",122031
-"cg03948744","chr16",122515
-"cg00079891","chr16",122716
-"cg09113560","chr16",122764
-"cg04995976","chr16",123198
-"cg06230303","chr16",123353
-"cg01262217","chr16",123363
-"cg04260507","chr16",123553
-"cg17199481","chr16",123676
-"cg01422009","chr16",125896
-"cg03462322","chr16",126397
-"cg16383109","chr16",126403
-"cg03110993","chr16",126800
-"cg03492469","chr16",126855
-"cg05501742","chr16",126844
-"cg16003913","chr16",127072
-"cg04257263","chr16",127088
-"cg15017278","chr16",127401
-"cg02729269","chr16",127772
-"cg07395378","chr16",127904
-"cg01609171","chr16",127949
-"cg10009236","chr16",127968
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-"cg15768556","chr16",128630
-"cg05394456","chr16",129230
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