| Previous changeset 26:ac5415190777 (2017-02-15) Next changeset 28:c1bf6f112a19 (2017-03-20) |
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Commit message:
Uploaded |
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modified:
getGSMdata/getGSMdata.xml |
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removed:
getGSMdata/geo_data-05050b50d4f8/GEO/.Rhistory getGSMdata/geo_data-05050b50d4f8/GEO/._.DS_Store getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.R getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.xml getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._.DS_Store getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._input.csv getGSMdata/geo_data-05050b50d4f8/GEO/test-data/IlmnTable.csv getGSMdata/geo_data-05050b50d4f8/GEO/test-data/MetaTable.csv getGSMdata/geo_data-05050b50d4f8/GEO/test-data/gmTable.csv getGSMdata/geo_data-05050b50d4f8/GEO/test-data/input.csv getGSMdata/geo_data-05050b50d4f8/GEO/tool_dependencies.xml |
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| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/.Rhistory --- a/getGSMdata/geo_data-05050b50d4f8/GEO/.Rhistory Wed Feb 15 10:21:18 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/._.DS_Store |
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| Binary file getGSMdata/geo_data-05050b50d4f8/GEO/._.DS_Store has changed |
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| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.R --- a/getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.R Wed Feb 15 10:21:18 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] -MetaTable = args[2] -IlmnTable = args[3] -gmTable = args[4] - -TAB = fread(GSMTable) - -if (is.null(TAB)) { - stop("Must specify input files") -} else { - GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) - IlmnIDTable <- Table(GEODataTable) - MetaData <- data.frame(Meta(GEODataTable)) - - - write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t") -} - -hm450.hg19 <- getPlatform() - -IlmnInfo <- - data.table( - IlmnID = names(hm450.hg19), - CHR = as.data.frame(hm450.hg19@seqnames)$value, - BP = as.numeric(hm450.hg19@elementMetadata$probeStart) - ) - - -write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t") - - -if (length(TAB$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.csv(gmSet, gmTable, row.names = FALSE, sep = "\t") |
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| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.xml --- a/getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.xml Wed Feb 15 10:21:18 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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" "$MetaTable" "$IlmnTable" "$gmTable"</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="csv" name="MetaTable" label="MetaData.csv"/> - <data format="csv" name="IlmnTable" label="IlmnData.csv"/> - <data format="csv" name="gmTable" label="gmSet.csv"/> - </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="csv" name="MetaTable" label="test-data/MetaTable.csv"/> - <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/> - <output format="csv" name="gmTable" label="test-data/gmTable.csv"/> - </test> - </tests> - <help> -**Description** -</help> -<citations> -GEO -</citations> -</tool> |
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| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._.DS_Store |
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| Binary file getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._.DS_Store has changed |
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| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._input.csv |
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| Binary file getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._input.csv has changed |
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| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/IlmnTable.csv --- a/getGSMdata/geo_data-05050b50d4f8/GEO/test-data/IlmnTable.csv Wed Feb 15 10:21:18 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,485578 +0,0 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|
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| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/MetaTable.csv --- a/getGSMdata/geo_data-05050b50d4f8/GEO/test-data/MetaTable.csv Wed Feb 15 10:21:18 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -"channel_count","characteristics_ch1","contact_address","contact_city","contact_country","contact_department","contact_institute","contact_name","contact_zip.postal_code","data_processing","data_row_count","description","extract_protocol_ch1","geo_accession","hyb_protocol","label_ch1","label_protocol_ch1","last_update_date","molecule_ch1","organism_ch1","platform_id","scan_protocol","series_id","source_name_ch1","status","submission_date","supplementary_file","taxid_ch1","title","type" -"1","sample type: melanoma cell line","Barngatan 2B","Lund","Sweden","Dept of Oncology","Lund University","Martin,,Lauss","22185","Raw intensities for methylated (M) and unmethylated (U) signal were extracted from Illumina’s GenomeStudio. Beta-values were calculated as M/(M+U). A total of 496 missing values (melanomas) were imputed using k-nearest neighbor imputation (k=10). For each sample we performed a peak-based correction of Illumina I and II chemical assays. For both assays we smoothed the beta values (Epanechnikov smoothing kernel) to estimate unmethylated and methylated peaks, respectively; and the unmethylated peak was moved to 0 and the methylated peak to 1 using linear scaling, with beta-values in between stretched accordingly. Beta-values below 0 were set back to 0 and values above 1 were set to 1.","485577","melanoma cell line","Genomic DNA was extracted from the biopsies using QIAamp DNA Mini Kit (Qiagen). A total of 500 ng of DNA were used for bisulfite treatment, using the EZ DNA Methylation Kit (Zymo). We hybridized 200 ng in 4 μl to the Infinium Human Methylation450 BeadChip array.","GSM1247787","Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol","Cy5 and Cy3","Standard Illumina Protocol","May 17 2015","genomic DNA","Homo sapiens","GPL13534","Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","GSE51547","SKMEL3","Public on May 17 2015","Oct 22 2013","NONE","9606","genomic DNA from Sample SKMEL3","genomic" |
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| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/gmTable.csv --- a/getGSMdata/geo_data-05050b50d4f8/GEO/test-data/gmTable.csv Wed Feb 15 10:21:18 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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|
| b |
| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/input.csv --- a/getGSMdata/geo_data-05050b50d4f8/GEO/test-data/input.csv Wed Feb 15 10:21:18 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -ID,Phenotype -GSM1247787,melanoma -GSM1247784,melanoma -GSM1247733,healthy |
| b |
| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/geo_data-05050b50d4f8/GEO/tool_dependencies.xml --- a/getGSMdata/geo_data-05050b50d4f8/GEO/tool_dependencies.xml Wed Feb 15 10:21:18 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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| b |
| diff -r ac5415190777 -r fd7bfd438a65 getGSMdata/getGSMdata.xml --- a/getGSMdata/getGSMdata.xml Wed Feb 15 10:21:18 2017 -0500 +++ b/getGSMdata/getGSMdata.xml Wed Feb 15 12:27:24 2017 -0500 |
| b |
| @@ -13,7 +13,7 @@ <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> </inputs> <outputs> - <data format="tab" name="GSMTable" label="GSMTable.tab"/> + <data format="txt" name="GSMTable" label="GSMTable.txt"/> </outputs> <tests> <test> |