| Previous changeset 7:3eb1073638d7 (2017-02-06) Next changeset 9:a376481b54b8 (2017-02-06) |
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getGSMdata/.Rhistory getGSMdata/._.DS_Store getGSMdata/getGSMdata.R getGSMdata/getGSMdata.xml getGSMdata/test-data/._.DS_Store getGSMdata/test-data/GSMTable.txt getGSMdata/tool_dependencies.xml |
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| diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/.Rhistory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGSMdata/.Rhistory Mon Feb 06 05:17:56 2017 -0500 |
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| @@ -0,0 +1,17 @@ +GSMTable <- ("test-data/GSMTable.txt") +write.table(samples, GSMTable, row.names = FALSE, sep = "\t") +?write.table +GSE <- "GSE51547" +search1 <- entrez_search(db = "gds", term = GSE, retmax = 1) +require("rentrez", quietly = TRUE) +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) +write.table(samples, file=GSMTable.txt, row.names = FALSE, sep = "\t",quote = FALSE) +write.table(samples, file="GSMTable.txt", row.names = FALSE, sep = "\t",quote = FALSE) |
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| diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/._.DS_Store |
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| Binary file getGSMdata/._.DS_Store has changed |
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| diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/getGSMdata.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGSMdata/getGSMdata.R Mon Feb 06 05:17:56 2017 -0500 |
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| @@ -0,0 +1,20 @@ +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) + |
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| diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/getGSMdata.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGSMdata/getGSMdata.xml Mon Feb 06 05:17:56 2017 -0500 |
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| @@ -0,0 +1,37 @@ +<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> |
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| diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/test-data/._.DS_Store |
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| Binary file getGSMdata/test-data/._.DS_Store has changed |
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| diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/test-data/GSMTable.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGSMdata/test-data/GSMTable.txt Mon Feb 06 05:17:56 2017 -0500 |
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| @@ -0,0 +1,71 @@ +ID Phenotype +GSM1247797 genomic DNA from Sample HEM.d_gDNA_2 +GSM1247734 genomic DNA from Sample MM37 +GSM1247757 genomic DNA from Sample MM10 +GSM1247794 genomic DNA from Sample HEM.m_gDNA_1 +GSM1247771 genomic DNA from Sample MM52 +GSM1247765 genomic DNA from Sample MM93 +GSM1247768 genomic DNA from Sample MM08 +GSM1247752 genomic DNA from Sample MM17 +GSM1247749 genomic DNA from Sample MM25 +GSM1247789 genomic DNA from Sample HT144 +GSM1247792 genomic DNA from Sample HEM.l_gDNA_1 +GSM1247774 genomic DNA from Sample MM57 +GSM1247751 genomic DNA from Sample MM19 +GSM1247800 genomic DNA from Sample HDF.a_gDNA_1 +GSM1247777 genomic DNA from Sample MM78 +GSM1247760 genomic DNA from Sample MM80 +GSM1247754 genomic DNA from Sample MM01 +GSM1247763 genomic DNA from Sample MM68 +GSM1247786 genomic DNA from Sample MM383 +GSM1247784 genomic DNA from Sample SKMEL5 +GSM1247787 genomic DNA from Sample SKMEL3 +GSM1247747 genomic DNA from Sample MM71 +GSM1247741 genomic DNA from Sample MM60 +GSM1247778 genomic DNA from Sample MM50 +GSM1247744 genomic DNA from Sample MM09 +GSM1247755 genomic DNA from Sample MM58 +GSM1247781 genomic DNA from Sample MM53 +GSM1247758 genomic DNA from Sample MM94 +GSM1247742 genomic DNA from Sample MM43 +GSM1247795 genomic DNA from Sample HEM.m_gDNA_2 +GSM1247779 genomic DNA from Sample MM16 +GSM1247802 genomic DNA from Sample Blood +GSM1247736 genomic DNA from Sample MM03 +GSM1247739 genomic DNA from Sample MM38 +GSM1247776 genomic DNA from Sample MM95 +GSM1247733 genomic DNA from Sample MM44 +GSM1247770 genomic DNA from Sample MM18 +GSM1247750 genomic DNA from Sample MM11 +GSM1247773 genomic DNA from Sample MM21 +GSM1247745 genomic DNA from Sample MM47 +GSM1247748 genomic DNA from Sample MM61 +GSM1247788 genomic DNA from Sample A7 +GSM1247791 genomic DNA from Sample CHL1 +GSM1247785 genomic DNA from Sample WM852 +GSM1247780 genomic DNA from Sample MM40 +GSM1247783 genomic DNA from Sample A2058 +GSM1247766 genomic DNA from Sample MM24 +GSM1247761 genomic DNA from Sample MM42 +GSM1247746 genomic DNA from Sample MM22 +GSM1247769 genomic DNA from Sample MM27 +GSM1247764 genomic DNA from Sample MM51 +GSM1247772 genomic DNA from Sample MM31 +GSM1247767 genomic DNA from Sample MM34 +GSM1247738 genomic DNA from Sample MM13 +GSM1247735 genomic DNA from Sample MM04 +GSM1247743 genomic DNA from Sample MM20 +GSM1247737 genomic DNA from Sample MM41 +GSM1247799 genomic DNA from Sample HEK.a_gDNA_2 +GSM1247740 genomic DNA from Sample MM81 +GSM1247793 genomic DNA from Sample HEM.l_gDNA_2 +GSM1247796 genomic DNA from Sample HEM.d_gDNA_1 +GSM1247790 genomic DNA from Sample WM239A +GSM1247775 genomic DNA from Sample MM02 +GSM1247798 genomic DNA from Sample HEK.a_gDNA_1 +GSM1247801 genomic DNA from Sample HDF.a_gDNA_2 +GSM1247756 genomic DNA from Sample MM82 +GSM1247759 genomic DNA from Sample MM14 +GSM1247782 genomic DNA from Sample MM86 +GSM1247762 genomic DNA from Sample MM45 +GSM1247753 genomic DNA from Sample MM83 |
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| diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGSMdata/tool_dependencies.xml Mon Feb 06 05:17:56 2017 -0500 |
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| @@ -0,0 +1,6 @@ +<?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> |