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Commit message:
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added:
GRsetFromGEO/.Rapp.history GRsetFromGEO/.Rhistory GRsetFromGEO/GRsetFromGEO.R GRsetFromGEO/GRsetFromGEO.xml GRsetFromGEO/test-data/out.RData |
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removed:
getGRsetFromGEO/.Rapp.history getGRsetFromGEO/.Rhistory getGRsetFromGEO/._.DS_Store getGRsetFromGEO/getGRsetFromGEO.R getGRsetFromGEO/getGRsetFromGEO.xml getGRsetFromGEO/test-data/._.DS_Store getGRsetFromGEO/test-data/out.RData |
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| diff -r 86777f72f33c -r 7511130b5068 GRsetFromGEO/.Rhistory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/.Rhistory Sun Jun 11 07:49:41 2017 -0400 |
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| @@ -0,0 +1,16 @@ +require("minfi", quietly = TRUE) +?require +require("minfi", quietly = TRUE) +minfi +as.data.frame(GRset) +GRset <- getGenomicRatioSetFromGEO(GSE) +getGenomicRatioSetFromGEO +require("minfi", quietly = TRUE) +options(warn = -1) +options("download.file.method"="wget") +args <- commandArgs(trailingOnly = TRUE) +GSE = args[1] +output = args[2] +GRset <- getGenomicRatioSetFromGEO(GSE) +save(GRset,file = output) +sessionInfo() |
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| diff -r 86777f72f33c -r 7511130b5068 GRsetFromGEO/GRsetFromGEO.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/GRsetFromGEO.R Sun Jun 11 07:49:41 2017 -0400 |
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| @@ -0,0 +1,12 @@ +require("minfi", quietly = TRUE) + +options(warn = -1) +options("download.file.method"="wget") + +args <- commandArgs(trailingOnly = TRUE) +GSE = args[1] +output = args[2] + +GRset <- getGenomicRatioSetFromGEO(GSE) + +save(GRset,file = output) |
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| diff -r 86777f72f33c -r 7511130b5068 GRsetFromGEO/GRsetFromGEO.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/GRsetFromGEO.xml Sun Jun 11 07:49:41 2017 -0400 |
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| @@ -0,0 +1,39 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="GetGEO" name="GRsetFromGEO" version="1.16.2"> + <requirements> + <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> + </requirements> +<stdio> + <exit_code range="1:" /> +</stdio> + <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> + <inputs> + <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> + </inputs> + <outputs> + <data format="RDdata" name="output" label="GRsetFromGEO.RData"/> + </outputs> + <tests> + <test> + <param name="test"> + <element name="test-data"> + <collection type="data"> + <element name="GSE" value="GSE51547"/> + </collection> + </element> + </param> + <output type="data" format="RData" name="output" label="test-data/out.RData"/> + </test> + </tests> + <help> + **What it does** + This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object + **Input** + The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" + **Output** + GenomicRatioSet object + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu049</citation> + </citations> +</tool> |
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| diff -r 86777f72f33c -r 7511130b5068 GRsetFromGEO/test-data/out.RData |
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| diff -r 86777f72f33c -r 7511130b5068 getGRsetFromGEO/.Rhistory --- a/getGRsetFromGEO/.Rhistory Sun Jun 11 06:38:17 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ -require("minfi", quietly = TRUE) -?require -require("minfi", quietly = TRUE) -minfi -as.data.frame(GRset) -GRset <- getGenomicRatioSetFromGEO(GSE) -getGenomicRatioSetFromGEO -require("minfi", quietly = TRUE) -options(warn = -1) -options("download.file.method"="wget") -args <- commandArgs(trailingOnly = TRUE) -GSE = args[1] -output = args[2] -GRset <- getGenomicRatioSetFromGEO(GSE) -save(GRset,file = output) -sessionInfo() |
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| diff -r 86777f72f33c -r 7511130b5068 getGRsetFromGEO/._.DS_Store |
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| diff -r 86777f72f33c -r 7511130b5068 getGRsetFromGEO/getGRsetFromGEO.R --- a/getGRsetFromGEO/getGRsetFromGEO.R Sun Jun 11 06:38:17 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -require("minfi", quietly = TRUE) - -options(warn = -1) -options("download.file.method"="wget") - -args <- commandArgs(trailingOnly = TRUE) -GSE = args[1] -output = args[2] - -GRset <- getGenomicRatioSetFromGEO(GSE) - -save(GRset,file = output) |
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| diff -r 86777f72f33c -r 7511130b5068 getGRsetFromGEO/getGRsetFromGEO.xml --- a/getGRsetFromGEO/getGRsetFromGEO.xml Sun Jun 11 06:38:17 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,39 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<tool id="getGRsetFromGEO" name="getGRsetFromGEO" version="1.18.4"> - <requirements> - <requirement type="package" version="1.20.0">bioconductor-minfi</requirement> - </requirements> -<stdio> - <exit_code range="1:" /> -</stdio> - <command> Rscript $__tool_directory__/getGRsetFromGEO.R "$GSE" "$output" </command> - <inputs> - <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> - </inputs> - <outputs> - <data format="RDdata" name="output" label="getGRsetFromGEO.RData"/> - </outputs> - <tests> - <test> - <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSE" value="GSE51547"/> - </collection> - </element> - </param> - <output type="data" format="RData" name="output" label="test-data/out.RData"/> - </test> - </tests> - <help> -**What it does** -This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object -**Input** -The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'" -**Output** -GenomicRatioSet object -</help> -<citations> -<citation type="doi">10.1093/bioinformatics/btu049</citation> -</citations> -</tool> |
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