| Previous changeset 10:f29602ae449e (2021-07-09) Next changeset 12:fe3ca740a485 (2022-09-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e |
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modified:
annotateMyIDs.xml test-data/out_gokegg.tab test-data/out_gokegg_dupsrem.tab test-data/out_rscript.txt |
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added:
test-data/genelist_arabidopsis.txt test-data/out_arabidopsis.tab |
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| diff -r f29602ae449e -r 4f2967b27e67 annotateMyIDs.xml --- a/annotateMyIDs.xml Fri Jul 09 14:20:02 2021 +0000 +++ b/annotateMyIDs.xml Fri Jul 01 12:24:49 2022 +0000 |
| [ |
| @@ -1,11 +1,15 @@ -<tool id="annotatemyids" name="annotateMyIDs" version="3.12.0+galaxy1"> +<tool id="annotatemyids" name="annotateMyIDs" version="3.14.0+galaxy0"> <description>annotate a generic set of identifiers</description> + <xrefs> + <xref type="bio.tools">annotatemyids</xref> + </xrefs> <requirements> - <requirement type="package" version="3.12.0">bioconductor-org.hs.eg.db</requirement> - <requirement type="package" version="3.12.0">bioconductor-org.mm.eg.db</requirement> - <requirement type="package" version="3.12.0">bioconductor-org.dm.eg.db</requirement> - <requirement type="package" version="3.12.0">bioconductor-org.dr.eg.db</requirement> - <requirement type="package" version="3.12.0">bioconductor-org.rn.eg.db</requirement> + <requirement type="package" version="3.14.0">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="3.14.0">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="3.14.0">bioconductor-org.dm.eg.db</requirement> + <requirement type="package" version="3.14.0">bioconductor-org.dr.eg.db</requirement> + <requirement type="package" version="3.14.0">bioconductor-org.rn.eg.db</requirement> + <requirement type="package" version="3.14.0">bioconductor-org.at.tair.db</requirement> </requirements> <version_command><![CDATA[ echo $(R --version | grep version | grep -v GNU)", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Rn.eg.db version" $(R --vanilla --slave -e "library(org.Rn.eg.db); cat(sessionInfo()\$otherPkgs\$org.Rn.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ") @@ -48,6 +52,9 @@ } else if (organism == "Rn"){ suppressPackageStartupMessages(library(org.Rn.eg.db)) db <- org.Rn.eg.db +} else if (organism == "At"){ + suppressPackageStartupMessages(library(org.At.tair.db)) + db <- org.At.tair.db } else { cat(paste("Organism type not supported", organism)) } @@ -72,6 +79,7 @@ <option value="Rn">Rat</option> <option value="Dm">Fruit fly</option> <option value="Dr">Zebrafish</option> + <option value="At">Arabidopsis thaliana</option> </param> <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file"> <option value="ENSEMBL" selected="true">Ensembl Gene</option> @@ -141,6 +149,14 @@ <param name="remove_dups" value="True" /> <output name="out_tab" file="out_gokegg_dupsrem.tab" /> </test> + <!-- Arabidopsis database --> + <test expect_num_outputs="1"> + <param name="id_file" value="genelist_arabidopsis.txt" ftype="tabular"/> + <param name="id_type" value="SYMBOL"/> + <param name="organism" value="At"/> + <param name="output_cols" value="GO,ENTREZID" /> + <output name="out_tab" file="out_arabidopsis.tab" /> + </test> </tests> <help><![CDATA[ |
| b |
| diff -r f29602ae449e -r 4f2967b27e67 test-data/genelist_arabidopsis.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genelist_arabidopsis.txt Fri Jul 01 12:24:49 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +CLE13 +TAF2 +UGT89B1 +KIN14P |
| b |
| diff -r f29602ae449e -r 4f2967b27e67 test-data/out_arabidopsis.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_arabidopsis.tab Fri Jul 01 12:24:49 2022 +0000 |
| b |
| @@ -0,0 +1,30 @@ +SYMBOL GO EVIDENCE ONTOLOGY ENTREZID +CLE13 GO:0005739 ISM CC 843734 +CLE13 GO:0010078 IDA BP 843734 +CLE13 GO:0010088 IDA BP 843734 +CLE13 GO:0033612 ISS MF 843734 +CLE13 GO:0045168 ISS BP 843734 +CLE13 GO:0045595 IDA BP 843734 +CLE13 GO:0048046 ISM CC 843734 +CLE13 GO:0048046 ISS CC 843734 +TAF2 GO:0000976 IBA MF 843733 +TAF2 GO:0003682 IBA MF 843733 +TAF2 GO:0005634 ISM CC 843733 +TAF2 GO:0005669 IBA CC 843733 +TAF2 GO:0005669 IEA CC 843733 +TAF2 GO:0006367 IBA BP 843733 +TAF2 GO:0008237 IEA MF 843733 +TAF2 GO:0008270 IEA MF 843733 +TAF2 GO:0009506 HDA CC 843733 +TAF2 GO:0016251 IBA MF 843733 +UGT89B1 GO:0005634 ISM CC 843725 +UGT89B1 GO:0016757 ISS MF 843725 +UGT89B1 GO:0033836 IEA MF 843725 +UGT89B1 GO:0035251 IDA MF 843725 +UGT89B1 GO:0047893 IEA MF 843725 +UGT89B1 GO:0080043 IDA MF 843725 +UGT89B1 GO:0080044 IDA MF 843725 +UGT89B1 GO:0080046 IDA MF 843725 +UGT89B1 GO:0102360 IEA MF 843725 +UGT89B1 GO:0102425 IEA MF 843725 +KIN14P NA NA NA NA |
| b |
| diff -r f29602ae449e -r 4f2967b27e67 test-data/out_gokegg.tab --- a/test-data/out_gokegg.tab Fri Jul 09 14:20:02 2021 +0000 +++ b/test-data/out_gokegg.tab Fri Jul 01 12:24:49 2022 +0000 |
| b |
| b'@@ -1,13 +1,12 @@\n ENSEMBL\tGO\tONTOLOGY\tEVIDENCE\n ENSG00000091831\tGO:0000122\tBP\tIMP\n-ENSG00000091831\tGO:0000790\tCC\tIBA\n-ENSG00000091831\tGO:0000790\tCC\tIDA\n-ENSG00000091831\tGO:0000790\tCC\tISA\n+ENSG00000091831\tGO:0000785\tCC\tIDA\n+ENSG00000091831\tGO:0000785\tCC\tISA\n ENSG00000091831\tGO:0000978\tMF\tIBA\n ENSG00000091831\tGO:0000978\tMF\tIDA\n ENSG00000091831\tGO:0000981\tMF\tISA\n-ENSG00000091831\tGO:0000981\tMF\tISM\n ENSG00000091831\tGO:0001093\tMF\tIPI\n+ENSG00000091831\tGO:0001222\tMF\tIPI\n ENSG00000091831\tGO:0001223\tMF\tIPI\n ENSG00000091831\tGO:0001228\tMF\tIDA\n ENSG00000091831\tGO:0001547\tBP\tIEA\n@@ -25,11 +24,10 @@\n ENSG00000091831\tGO:0005794\tCC\tIEA\n ENSG00000091831\tGO:0005829\tCC\tTAS\n ENSG00000091831\tGO:0005886\tCC\tIDA\n+ENSG00000091831\tGO:0005886\tCC\tTAS\n ENSG00000091831\tGO:0006338\tBP\tNAS\n ENSG00000091831\tGO:0006355\tBP\tNAS\n ENSG00000091831\tGO:0006357\tBP\tIBA\n-ENSG00000091831\tGO:0006357\tBP\tTAS\n-ENSG00000091831\tGO:0006367\tBP\tTAS\n ENSG00000091831\tGO:0007165\tBP\tTAS\n ENSG00000091831\tGO:0007200\tBP\tISS\n ENSG00000091831\tGO:0007204\tBP\tISS\n@@ -42,11 +40,9 @@\n ENSG00000091831\tGO:0010863\tBP\tISS\n ENSG00000091831\tGO:0016020\tCC\tNAS\n ENSG00000091831\tGO:0016021\tCC\tIEA\n-ENSG00000091831\tGO:0016579\tBP\tTAS\n ENSG00000091831\tGO:0017025\tMF\tIPI\n ENSG00000091831\tGO:0019899\tMF\tIPI\n ENSG00000091831\tGO:0019901\tMF\tIPI\n-ENSG00000091831\tGO:0030111\tBP\tTAS\n ENSG00000091831\tGO:0030235\tMF\tNAS\n ENSG00000091831\tGO:0030284\tMF\tIDA\n ENSG00000091831\tGO:0030284\tMF\tNAS\n@@ -59,7 +55,6 @@\n ENSG00000091831\tGO:0032355\tBP\tIDA\n ENSG00000091831\tGO:0032991\tCC\tIDA\n ENSG00000091831\tGO:0032991\tCC\tIMP\n-ENSG00000091831\tGO:0033146\tBP\tTAS\n ENSG00000091831\tGO:0034056\tMF\tIDA\n ENSG00000091831\tGO:0034121\tBP\tIEA\n ENSG00000091831\tGO:0035327\tCC\tIDA\n@@ -76,7 +71,6 @@\n ENSG00000091831\tGO:0050727\tBP\tIEA\n ENSG00000091831\tGO:0051091\tBP\tIDA\n ENSG00000091831\tGO:0051117\tMF\tIDA\n-ENSG00000091831\tGO:0051897\tBP\tTAS\n ENSG00000091831\tGO:0060065\tBP\tIEA\n ENSG00000091831\tGO:0060068\tBP\tIEA\n ENSG00000091831\tGO:0060523\tBP\tIEA\n@@ -92,30 +86,27 @@\n ENSG00000091831\tGO:0097550\tCC\tIDA\n ENSG00000091831\tGO:1903799\tBP\tIMP\n ENSG00000091831\tGO:1990837\tMF\tIDA\n-ENSG00000082175\tGO:0000790\tCC\tIBA\n-ENSG00000082175\tGO:0000790\tCC\tISA\n+ENSG00000082175\tGO:0000785\tCC\tISA\n ENSG00000082175\tGO:0000978\tMF\tIBA\n ENSG00000082175\tGO:0000978\tMF\tIDA\n ENSG00000082175\tGO:0000981\tMF\tISA\n-ENSG00000082175\tGO:0000981\tMF\tISM\n-ENSG00000082175\tGO:0001225\tMF\tIPI\n+ENSG00000082175\tGO:0001223\tMF\tIPI\n ENSG00000082175\tGO:0001228\tMF\tIDA\n ENSG00000082175\tGO:0001542\tBP\tIEA\n ENSG00000082175\tGO:0002070\tBP\tIEA\n ENSG00000082175\tGO:0003677\tMF\tTAS\n ENSG00000082175\tGO:0003707\tMF\tIEA\n ENSG00000082175\tGO:0004879\tMF\tIBA\n-ENSG00000082175\tGO:0004879\tMF\tIEA\n ENSG00000082175\tGO:0005496\tMF\tIEA\n ENSG00000082175\tGO:0005515\tMF\tIPI\n ENSG00000082175\tGO:0005654\tCC\tTAS\n ENSG00000082175\tGO:0005741\tCC\tIEA\n ENSG00000082175\tGO:0005829\tCC\tTAS\n ENSG00000082175\tGO:0006357\tBP\tIBA\n-ENSG00000082175\tGO:0006367\tBP\tTAS\n ENSG00000082175\tGO:0007165\tBP\tTAS\n ENSG00000082175\tGO:0007267\tBP\tTAS\n ENSG00000082175\tGO:0008270\tMF\tIEA\n+ENSG00000082175\tGO:0010628\tBP\tNAS\n ENSG00000082175\tGO:0010629\tBP\tIEP\n ENSG00000082175\tGO:0019899\tMF\tIPI\n ENSG00000082175\tGO:0030518\tBP\tIBA\n@@ -127,7 +118,6 @@\n ENSG00000082175\tGO:0050847\tBP\tIEA\n ENSG00000082175\tGO:0051117\tMF\tIDA\n ENSG00000082175\tGO:0060748\tBP\tIEA\n-ENSG00000141736\tGO:0000165\tBP\tTAS\n ENSG00000141736\tGO:0001042\tMF\tIDA\n ENSG00000141736\tGO:0001934\tBP\tISS\n ENSG00000141736\tGO:0004713\tMF\tIDA\n@@ -145,7 +135,6 @@\n ENSG00000141736\tGO:0005886\tCC\tNAS\n ENSG00000141736\tGO:0005886\tCC\tTAS\n ENSG00000141736\tGO:0005887\tCC\tIBA\n-ENSG00000141736\tGO:0006357\tBP\tTAS\n ENSG00000141736\tGO:0006468\tBP\tTAS\n ENSG00000141736\tGO:0007165\tBP\tIDA\n ENSG00000141736\tGO:0007166\tBP\tIDA\n@@ -175,7 +164,6 @@\n ENSG00000141736\tGO:0033088\tBP\tIEA\n ENSG00000141736\tGO:0033674\tBP\tIBA\n ENSG00000141736\tGO:0035556\tBP\tIDA\n-ENSG00000141736\tGO:0038128\tBP\tTAS\n ENSG00000141736\tGO:0038143\tCC\tIDA\n ENSG00000141736\tGO:0042060\tBP\tIDA\n ENSG00000141736\tGO:0042552\tBP\tIEA\n@@ -197,18 +185,15 @@\n ENSG00000141736\tGO:0048471\tCC\tIEA\n ENSG00000141736\tGO:0048709\tB'..b'@@ -621,17 +588,15 @@\n ENSG00000141510\tGO:0006302\tBP\tIEA\n ENSG00000141510\tGO:0006355\tBP\tIDA\n ENSG00000141510\tGO:0006355\tBP\tIMP\n+ENSG00000141510\tGO:0006357\tBP\tIBA\n ENSG00000141510\tGO:0006606\tBP\tIEA\n ENSG00000141510\tGO:0006914\tBP\tIMP\n ENSG00000141510\tGO:0006974\tBP\tIDA\n ENSG00000141510\tGO:0006974\tBP\tIMP\n ENSG00000141510\tGO:0006977\tBP\tIMP\n-ENSG00000141510\tGO:0006977\tBP\tTAS\n ENSG00000141510\tGO:0006978\tBP\tIDA\n ENSG00000141510\tGO:0006978\tBP\tIMP\n ENSG00000141510\tGO:0006983\tBP\tIDA\n-ENSG00000141510\tGO:0007050\tBP\tIDA\n-ENSG00000141510\tGO:0007050\tBP\tIMP\n ENSG00000141510\tGO:0007179\tBP\tIEA\n ENSG00000141510\tGO:0007265\tBP\tIEP\n ENSG00000141510\tGO:0007369\tBP\tIEA\n@@ -656,10 +621,8 @@\n ENSG00000141510\tGO:0010666\tBP\tIEA\n ENSG00000141510\tGO:0016032\tBP\tIMP\n ENSG00000141510\tGO:0016363\tCC\tIDA\n-ENSG00000141510\tGO:0016579\tBP\tTAS\n ENSG00000141510\tGO:0016604\tCC\tIDA\n ENSG00000141510\tGO:0016605\tCC\tIDA\n-ENSG00000141510\tGO:0019221\tBP\tTAS\n ENSG00000141510\tGO:0019899\tMF\tIPI\n ENSG00000141510\tGO:0019901\tMF\tIPI\n ENSG00000141510\tGO:0019903\tMF\tIPI\n@@ -673,7 +636,6 @@\n ENSG00000141510\tGO:0031497\tBP\tIDA\n ENSG00000141510\tGO:0031571\tBP\tIMP\n ENSG00000141510\tGO:0031625\tMF\tIPI\n-ENSG00000141510\tGO:0031965\tCC\tIDA\n ENSG00000141510\tGO:0032991\tCC\tIDA\n ENSG00000141510\tGO:0032991\tCC\tIMP\n ENSG00000141510\tGO:0033077\tBP\tIEA\n@@ -683,18 +645,18 @@\n ENSG00000141510\tGO:0035033\tMF\tIEA\n ENSG00000141510\tGO:0035035\tMF\tIPI\n ENSG00000141510\tGO:0035264\tBP\tIEA\n-ENSG00000141510\tGO:0035690\tBP\tIEP\n ENSG00000141510\tGO:0035794\tBP\tIEA\n ENSG00000141510\tGO:0035861\tCC\tIEA\n ENSG00000141510\tGO:0036003\tBP\tIDA\n+ENSG00000141510\tGO:0036310\tMF\tIDA\n ENSG00000141510\tGO:0042149\tBP\tIDA\n ENSG00000141510\tGO:0042771\tBP\tIDA\n ENSG00000141510\tGO:0042771\tBP\tIMP\n ENSG00000141510\tGO:0042802\tMF\tIPI\n ENSG00000141510\tGO:0042826\tMF\tIPI\n ENSG00000141510\tGO:0042981\tBP\tIDA\n-ENSG00000141510\tGO:0042981\tBP\tTAS\n ENSG00000141510\tGO:0043065\tBP\tIDA\n+ENSG00000141510\tGO:0043066\tBP\tIGI\n ENSG00000141510\tGO:0043066\tBP\tIMP\n ENSG00000141510\tGO:0043153\tBP\tISS\n ENSG00000141510\tGO:0043504\tBP\tIEA\n@@ -711,7 +673,6 @@\n ENSG00000141510\tGO:0045944\tBP\tIGI\n ENSG00000141510\tGO:0045944\tBP\tIMP\n ENSG00000141510\tGO:0046677\tBP\tIEP\n-ENSG00000141510\tGO:0046827\tBP\tTAS\n ENSG00000141510\tGO:0046982\tMF\tIPI\n ENSG00000141510\tGO:0047485\tMF\tIPI\n ENSG00000141510\tGO:0048147\tBP\tIMP\n@@ -725,23 +686,25 @@\n ENSG00000141510\tGO:0051262\tBP\tIEA\n ENSG00000141510\tGO:0051402\tBP\tIEA\n ENSG00000141510\tGO:0051721\tMF\tIPI\n+ENSG00000141510\tGO:0051726\tBP\tIDA\n+ENSG00000141510\tGO:0051726\tBP\tIGI\n+ENSG00000141510\tGO:0051726\tBP\tIMP\n+ENSG00000141510\tGO:0051726\tBP\tISS\n ENSG00000141510\tGO:0051974\tBP\tIDA\n ENSG00000141510\tGO:0060218\tBP\tIMP\n ENSG00000141510\tGO:0060333\tBP\tIEA\n ENSG00000141510\tGO:0060411\tBP\tIEA\n ENSG00000141510\tGO:0061419\tBP\tIEA\n+ENSG00000141510\tGO:0061629\tMF\tIPI\n+ENSG00000141510\tGO:0062100\tBP\tIEA\n ENSG00000141510\tGO:0065003\tBP\tIDA\n ENSG00000141510\tGO:0070059\tBP\tIEA\n ENSG00000141510\tGO:0070245\tBP\tISS\n ENSG00000141510\tGO:0070266\tBP\tIEA\n-ENSG00000141510\tGO:0071158\tBP\tIDA\n-ENSG00000141510\tGO:0071158\tBP\tIGI\n-ENSG00000141510\tGO:0071158\tBP\tIMP\n ENSG00000141510\tGO:0071456\tBP\tIEP\n ENSG00000141510\tGO:0071479\tBP\tIMP\n ENSG00000141510\tGO:0071480\tBP\tIDA\n ENSG00000141510\tGO:0071494\tBP\tIEA\n-ENSG00000141510\tGO:0071850\tBP\tIEA\n ENSG00000141510\tGO:0072331\tBP\tIDA\n ENSG00000141510\tGO:0072332\tBP\tIMP\n ENSG00000141510\tGO:0072717\tBP\tIDA\n@@ -753,17 +716,16 @@\n ENSG00000141510\tGO:0097252\tBP\tIDA\n ENSG00000141510\tGO:0097371\tMF\tIEA\n ENSG00000141510\tGO:0097718\tMF\tIPI\n+ENSG00000141510\tGO:0140296\tMF\tIPI\n ENSG00000141510\tGO:1900119\tBP\tIMP\n-ENSG00000141510\tGO:1900740\tBP\tTAS\n ENSG00000141510\tGO:1901525\tBP\tIEA\n-ENSG00000141510\tGO:1901796\tBP\tTAS\n ENSG00000141510\tGO:1902108\tBP\tIEA\n ENSG00000141510\tGO:1902253\tBP\tIEA\n-ENSG00000141510\tGO:1902749\tBP\tTAS\n ENSG00000141510\tGO:1902895\tBP\tIDA\n ENSG00000141510\tGO:1902895\tBP\tIGI\n ENSG00000141510\tGO:1903799\tBP\tIEA\n ENSG00000141510\tGO:1903800\tBP\tIDA\n+ENSG00000141510\tGO:1903800\tBP\tIMP\n ENSG00000141510\tGO:1904024\tBP\tIEA\n ENSG00000141510\tGO:1905856\tBP\tIMP\n ENSG00000141510\tGO:1990144\tBP\tIEA\n' |
| b |
| diff -r f29602ae449e -r 4f2967b27e67 test-data/out_gokegg_dupsrem.tab --- a/test-data/out_gokegg_dupsrem.tab Fri Jul 09 14:20:02 2021 +0000 +++ b/test-data/out_gokegg_dupsrem.tab Fri Jul 01 12:24:49 2022 +0000 |
| b |
| @@ -1,7 +1,7 @@ ENSEMBL GO ONTOLOGY EVIDENCE ENSG00000091831 GO:0000122 BP IMP -ENSG00000082175 GO:0000790 CC IBA -ENSG00000141736 GO:0000165 BP TAS +ENSG00000082175 GO:0000785 CC ISA +ENSG00000141736 GO:0001042 MF IDA ENSG00000012048 GO:0000151 CC NAS ENSG00000139618 GO:0000722 BP IEA ENSG00000129514 GO:0000122 BP IEA |
| b |
| diff -r f29602ae449e -r 4f2967b27e67 test-data/out_rscript.txt --- a/test-data/out_rscript.txt Fri Jul 09 14:20:02 2021 +0000 +++ b/test-data/out_rscript.txt Fri Jul 01 12:24:49 2022 +0000 |
| [ |
| @@ -8,8 +8,10 @@ organism <- "Hs" output_cols <- "ENSEMBL,ENTREZID,SYMBOL,GENENAME" file_has_header <- FALSE +remove_dups <- FALSE -ids <- as.character(read.table("/tmp/tmpY5XREO/files/000/dataset_3.dat", header=file_has_header)[,1]) +input <- read.table('/tmp/tmpqa0_mcvo/files/3/1/c/dataset_31cbce15-3708-4c78-bdf6-aca07697ccb7.dat', header=file_has_header, sep="\t", quote="") +ids <- as.character(input[, 1]) if(organism == "Hs"){ suppressPackageStartupMessages(library(org.Hs.eg.db)) @@ -23,12 +25,23 @@ } else if (organism == "Dr"){ suppressPackageStartupMessages(library(org.Dr.eg.db)) db <- org.Dr.eg.db +} else if (organism == "Rn"){ + suppressPackageStartupMessages(library(org.Rn.eg.db)) + db <- org.Rn.eg.db +} else if (organism == "At"){ + suppressPackageStartupMessages(library(org.At.tair.db)) + db <- org.At.tair.db } else { cat(paste("Organism type not supported", organism)) } cols <- unlist(strsplit(output_cols, ",")) result <- select(db, keys=ids, keytype=id_type, columns=cols) -write.table(result, file="/tmp/tmpY5XREO/files/000/dataset_4.dat", sep="\t", row.names=FALSE, quote=FALSE) + +if(remove_dups) { + result <- result[!duplicated(result$ENSEMBL),] +} + +write.table(result, file='/tmp/tmpqa0_mcvo/job_working_directory/000/4/outputs/galaxy_dataset_b06fd1c6-69cb-4c43-9caf-1a445a3b8b2e.dat', sep="\t", row.names=FALSE, quote=FALSE) \ No newline at end of file |