| Previous changeset 3:1a125daea0d8 (2018-11-26) Next changeset 5:b467a89be0c6 (2019-02-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ec1ff890b79f39031a25040611363ef3de1bc5c2 |
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modified:
annotateMyIDs.xml test-data/out.tab test-data/out_gokegg.tab test-data/out_gokegg_dupsrem.tab |
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| diff -r 1a125daea0d8 -r 38eedf3cc3c9 annotateMyIDs.xml --- a/annotateMyIDs.xml Mon Nov 26 02:46:54 2018 -0500 +++ b/annotateMyIDs.xml Mon Jan 28 18:17:05 2019 -0500 |
| [ |
| @@ -1,10 +1,10 @@ -<tool id="annotatemyids" name="annotateMyIDs" version="3.5.0.1"> +<tool id="annotatemyids" name="annotateMyIDs" version="3.6.0"> <description>annotate a generic set of identifiers</description> <requirements> - <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> - <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> - <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement> - <requirement type="package" version="3.5.0">bioconductor-org.dr.eg.db</requirement> + <requirement type="package" version="3.6.0">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="3.6.0">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="3.6.0">bioconductor-org.dm.eg.db</requirement> + <requirement type="package" version="3.6.0">bioconductor-org.dr.eg.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: ") |
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| diff -r 1a125daea0d8 -r 38eedf3cc3c9 test-data/out.tab --- a/test-data/out.tab Mon Nov 26 02:46:54 2018 -0500 +++ b/test-data/out.tab Mon Jan 28 18:17:05 2019 -0500 |
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| @@ -6,4 +6,5 @@ BRCA2 ENSG00000139618 675 BRCA2, DNA repair associated FOXA1 ENSG00000129514 3169 forkhead box A1 PTEN ENSG00000171862 5728 phosphatase and tensin homolog +PTEN ENSG00000284792 5728 phosphatase and tensin homolog TP53 ENSG00000141510 7157 tumor protein p53 |
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| diff -r 1a125daea0d8 -r 38eedf3cc3c9 test-data/out_gokegg.tab --- a/test-data/out_gokegg.tab Mon Nov 26 02:46:54 2018 -0500 +++ b/test-data/out_gokegg.tab Mon Jan 28 18:17:05 2019 -0500 |
| b |
| b'@@ -2,6 +2,8 @@\n ENSG00000091831\tGO:0000122\tBP\tIMP\n ENSG00000091831\tGO:0000790\tCC\tIDA\n ENSG00000091831\tGO:0000978\tMF\tIDA\n+ENSG00000091831\tGO:0000981\tMF\tISM\n+ENSG00000091831\tGO:0000981\tMF\tNAS\n ENSG00000091831\tGO:0001046\tMF\tIDA\n ENSG00000091831\tGO:0001077\tMF\tIDA\n ENSG00000091831\tGO:0001093\tMF\tIPI\n@@ -17,6 +19,7 @@\n ENSG00000091831\tGO:0005654\tCC\tTAS\n ENSG00000091831\tGO:0005737\tCC\tIDA\n ENSG00000091831\tGO:0005794\tCC\tIEA\n+ENSG00000091831\tGO:0005829\tCC\tTAS\n ENSG00000091831\tGO:0005886\tCC\tIDA\n ENSG00000091831\tGO:0006338\tBP\tNAS\n ENSG00000091831\tGO:0006351\tBP\tTAS\n@@ -50,6 +53,7 @@\n ENSG00000091831\tGO:0030520\tBP\tIDA\n ENSG00000091831\tGO:0030520\tBP\tNAS\n ENSG00000091831\tGO:0032355\tBP\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@@ -59,17 +63,19 @@\n ENSG00000091831\tGO:0042802\tMF\tIPI\n ENSG00000091831\tGO:0042981\tBP\tIEA\n ENSG00000091831\tGO:0043124\tBP\tIDA\n-ENSG00000091831\tGO:0043234\tCC\tIMP\n ENSG00000091831\tGO:0043433\tBP\tIDA\n ENSG00000091831\tGO:0043627\tBP\tIDA\n ENSG00000091831\tGO:0045893\tBP\tIDA\n ENSG00000091831\tGO:0045899\tBP\tIDA\n ENSG00000091831\tGO:0045944\tBP\tIDA\n+ENSG00000091831\tGO:0046854\tBP\tIEA\n+ENSG00000091831\tGO:0046934\tMF\tTAS\n ENSG00000091831\tGO:0048146\tBP\tIEA\n ENSG00000091831\tGO:0048863\tBP\tIEA\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@@ -85,6 +91,8 @@\n ENSG00000091831\tGO:0097550\tCC\tIDA\n ENSG00000091831\tGO:1903799\tBP\tIMP\n ENSG00000082175\tGO:0000978\tMF\tIDA\n+ENSG00000082175\tGO:0000981\tMF\tISM\n+ENSG00000082175\tGO:0000981\tMF\tNAS\n ENSG00000082175\tGO:0001077\tMF\tIDA\n ENSG00000082175\tGO:0001542\tBP\tIEA\n ENSG00000082175\tGO:0002070\tBP\tIEA\n@@ -113,20 +121,27 @@\n ENSG00000141736\tGO:0000165\tBP\tTAS\n ENSG00000141736\tGO:0001042\tMF\tIDA\n ENSG00000141736\tGO:0001934\tBP\tISS\n+ENSG00000141736\tGO:0004709\tMF\tIBA\n+ENSG00000141736\tGO:0004713\tMF\tIBA\n ENSG00000141736\tGO:0004713\tMF\tIDA\n ENSG00000141736\tGO:0004713\tMF\tIGI\n ENSG00000141736\tGO:0004713\tMF\tTAS\n+ENSG00000141736\tGO:0004714\tMF\tIBA\n ENSG00000141736\tGO:0004714\tMF\tIDA\n ENSG00000141736\tGO:0004716\tMF\tIEA\n+ENSG00000141736\tGO:0004871\tMF\tIBA\n+ENSG00000141736\tGO:0004888\tMF\tIBA\n ENSG00000141736\tGO:0004888\tMF\tIDA\n ENSG00000141736\tGO:0005088\tMF\tTAS\n ENSG00000141736\tGO:0005515\tMF\tIPI\n ENSG00000141736\tGO:0005524\tMF\tIEA\n ENSG00000141736\tGO:0005634\tCC\tIDA\n+ENSG00000141736\tGO:0005737\tCC\tIBA\n ENSG00000141736\tGO:0005829\tCC\tIDA\n ENSG00000141736\tGO:0005886\tCC\tIDA\n ENSG00000141736\tGO:0005886\tCC\tNAS\n ENSG00000141736\tGO:0005886\tCC\tTAS\n+ENSG00000141736\tGO:0005887\tCC\tIBA\n ENSG00000141736\tGO:0006351\tBP\tIEA\n ENSG00000141736\tGO:0006357\tBP\tTAS\n ENSG00000141736\tGO:0006468\tBP\tTAS\n@@ -135,12 +150,15 @@\n ENSG00000141736\tGO:0007167\tBP\tTAS\n ENSG00000141736\tGO:0007169\tBP\tIDA\n ENSG00000141736\tGO:0007169\tBP\tTAS\n+ENSG00000141736\tGO:0007275\tBP\tIBA\n ENSG00000141736\tGO:0007422\tBP\tIEA\n ENSG00000141736\tGO:0007507\tBP\tIEA\n ENSG00000141736\tGO:0007528\tBP\tIEA\n ENSG00000141736\tGO:0008022\tMF\tIPI\n ENSG00000141736\tGO:0008045\tBP\tIEA\n ENSG00000141736\tGO:0008283\tBP\tTAS\n+ENSG00000141736\tGO:0009925\tCC\tIBA\n+ENSG00000141736\tGO:0009968\tBP\tIBA\n ENSG00000141736\tGO:0010008\tCC\tIDA\n ENSG00000141736\tGO:0014065\tBP\tIDA\n ENSG00000141736\tGO:0016021\tCC\tNAS\n@@ -149,18 +167,24 @@\n ENSG00000141736\tGO:0018108\tBP\tIEA\n ENSG00000141736\tGO:0019838\tMF\tIDA\n ENSG00000141736\tGO:0019903\tMF\tIPI\n+ENSG00000141736\tGO:0030154\tBP\tIBA\n ENSG00000141736\tGO:0030307\tBP\tIMP\n+ENSG00000141736\tGO:0031434\tMF\tIBA\n ENSG00000141736\tGO:0032886\tBP\tIDA\n ENSG00000141736\tGO:0033088\tBP\tIEA\n+ENSG00000141736\tGO:0033674\tBP\tIBA\n ENSG00000141736\tGO:0038128\tBP\tTAS\n ENSG00000141736\tGO:0042060\tBP\tIDA\n ENSG00000141736\tGO:0042552\tBP\tIEA\n ENSG00000141736\tGO:0042802\tMF\tIPI\n+ENSG00000141736\tGO:0043066\tBP\tIBA\n ENSG00000141736\tGO:0043125\tMF\tTAS\n ENSG00000141736\tGO:0043209\tCC\tIEA\n+ENSG00000141736\tGO:0043235\tCC\tIBA\n ENSG00000141736\tGO:0043235\t'..b':0002020\tMF\tIPI\n ENSG00000141510\tGO:0002039\tMF\tIPI\n+ENSG00000141510\tGO:0002687\tBP\tIEA\n ENSG00000141510\tGO:0003677\tMF\tIDA\n ENSG00000141510\tGO:0003677\tMF\tIMP\n ENSG00000141510\tGO:0003682\tMF\tIDA\n@@ -561,8 +613,6 @@\n ENSG00000141510\tGO:0006289\tBP\tIMP\n ENSG00000141510\tGO:0006355\tBP\tIDA\n ENSG00000141510\tGO:0006355\tBP\tIMP\n-ENSG00000141510\tGO:0006366\tBP\tIEA\n-ENSG00000141510\tGO:0006461\tBP\tIDA\n ENSG00000141510\tGO:0006914\tBP\tIMP\n ENSG00000141510\tGO:0006974\tBP\tIDA\n ENSG00000141510\tGO:0006977\tBP\tIMP\n@@ -575,6 +625,7 @@\n ENSG00000141510\tGO:0007265\tBP\tIEP\n ENSG00000141510\tGO:0007275\tBP\tIMP\n ENSG00000141510\tGO:0007569\tBP\tIMP\n+ENSG00000141510\tGO:0008022\tMF\tIEA\n ENSG00000141510\tGO:0008104\tBP\tIDA\n ENSG00000141510\tGO:0008134\tMF\tIPI\n ENSG00000141510\tGO:0008270\tMF\tTAS\n@@ -584,7 +635,9 @@\n ENSG00000141510\tGO:0008285\tBP\tISS\n ENSG00000141510\tGO:0008340\tBP\tISS\n ENSG00000141510\tGO:0009299\tBP\tIMP\n+ENSG00000141510\tGO:0010038\tBP\tIEA\n ENSG00000141510\tGO:0010165\tBP\tIBA\n+ENSG00000141510\tGO:0010224\tBP\tIEA\n ENSG00000141510\tGO:0010332\tBP\tIMP\n ENSG00000141510\tGO:0010628\tBP\tIDA\n ENSG00000141510\tGO:0010628\tBP\tIMP\n@@ -594,6 +647,7 @@\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@@ -602,14 +656,22 @@\n ENSG00000141510\tGO:0030330\tBP\tIDA\n ENSG00000141510\tGO:0030330\tBP\tIMP\n ENSG00000141510\tGO:0030971\tMF\tIPI\n+ENSG00000141510\tGO:0031000\tBP\tIEA\n ENSG00000141510\tGO:0031065\tBP\tIBA\n ENSG00000141510\tGO:0031497\tBP\tIDA\n ENSG00000141510\tGO:0031571\tBP\tIMP\n ENSG00000141510\tGO:0031625\tMF\tIPI\n ENSG00000141510\tGO:0032461\tBP\tIDA\n+ENSG00000141510\tGO:0032526\tBP\tIEA\n+ENSG00000141510\tGO:0032991\tCC\tIDA\n+ENSG00000141510\tGO:0032991\tCC\tIMP\n+ENSG00000141510\tGO:0033552\tBP\tIEA\n+ENSG00000141510\tGO:0034605\tBP\tIEA\n+ENSG00000141510\tGO:0034614\tBP\tIEA\n ENSG00000141510\tGO:0034644\tBP\tIDA\n ENSG00000141510\tGO:0035035\tMF\tIPI\n ENSG00000141510\tGO:0035690\tBP\tIEP\n+ENSG00000141510\tGO:0042060\tBP\tIEA\n ENSG00000141510\tGO:0042149\tBP\tIDA\n ENSG00000141510\tGO:0042771\tBP\tIDA\n ENSG00000141510\tGO:0042771\tBP\tIMP\n@@ -622,16 +684,17 @@\n ENSG00000141510\tGO:0043066\tBP\tIMP\n ENSG00000141510\tGO:0043153\tBP\tISS\n ENSG00000141510\tGO:0043161\tBP\tTAS\n-ENSG00000141510\tGO:0043234\tCC\tIDA\n-ENSG00000141510\tGO:0043234\tCC\tIMP\n+ENSG00000141510\tGO:0043200\tBP\tIEA\n ENSG00000141510\tGO:0043525\tBP\tIBA\n ENSG00000141510\tGO:0043621\tMF\tIPI\n ENSG00000141510\tGO:0044212\tMF\tIDA\n+ENSG00000141510\tGO:0045471\tBP\tIEA\n ENSG00000141510\tGO:0045892\tBP\tIDA\n ENSG00000141510\tGO:0045892\tBP\tIMP\n ENSG00000141510\tGO:0045892\tBP\tISS\n ENSG00000141510\tGO:0045893\tBP\tIDA\n ENSG00000141510\tGO:0045893\tBP\tIMP\n+ENSG00000141510\tGO:0045899\tBP\tIDA\n ENSG00000141510\tGO:0045944\tBP\tIDA\n ENSG00000141510\tGO:0045944\tBP\tIGI\n ENSG00000141510\tGO:0045944\tBP\tIMP\n@@ -642,13 +705,18 @@\n ENSG00000141510\tGO:0047485\tMF\tIPI\n ENSG00000141510\tGO:0048147\tBP\tIMP\n ENSG00000141510\tGO:0048512\tBP\tISS\n+ENSG00000141510\tGO:0048662\tBP\tIEA\n ENSG00000141510\tGO:0050731\tBP\tISS\n ENSG00000141510\tGO:0051087\tMF\tIPI\n ENSG00000141510\tGO:0051097\tBP\tTAS\n+ENSG00000141510\tGO:0051123\tBP\tIEA\n ENSG00000141510\tGO:0051262\tBP\tTAS\n ENSG00000141510\tGO:0051289\tBP\tIMP\n+ENSG00000141510\tGO:0051453\tBP\tIEA\n ENSG00000141510\tGO:0051721\tMF\tIPI\n ENSG00000141510\tGO:0051974\tBP\tIDA\n+ENSG00000141510\tGO:0055093\tBP\tIEA\n+ENSG00000141510\tGO:0065003\tBP\tIDA\n ENSG00000141510\tGO:0070245\tBP\tISS\n ENSG00000141510\tGO:0071158\tBP\tIDA\n ENSG00000141510\tGO:0071158\tBP\tIMP\n@@ -663,12 +731,14 @@\n ENSG00000141510\tGO:0090403\tBP\tIMP\n ENSG00000141510\tGO:0097193\tBP\tTAS\n ENSG00000141510\tGO:0097252\tBP\tIDA\n+ENSG00000141510\tGO:0097371\tMF\tIEA\n ENSG00000141510\tGO:0097718\tMF\tIPI\n ENSG00000141510\tGO:1900119\tBP\tIMP\n ENSG00000141510\tGO:1900740\tBP\tTAS\n ENSG00000141510\tGO:1901796\tBP\tTAS\n ENSG00000141510\tGO:1902749\tBP\tTAS\n ENSG00000141510\tGO:1902895\tBP\tIDA\n+ENSG00000141510\tGO:1903205\tBP\tIEA\n ENSG00000141510\tGO:1990440\tBP\tISS\n ENSG00000141510\tGO:2000379\tBP\tIMP\n ENSG00000141510\tGO:2001244\tBP\tIMP\n' |
| b |
| diff -r 1a125daea0d8 -r 38eedf3cc3c9 test-data/out_gokegg_dupsrem.tab --- a/test-data/out_gokegg_dupsrem.tab Mon Nov 26 02:46:54 2018 -0500 +++ b/test-data/out_gokegg_dupsrem.tab Mon Jan 28 18:17:05 2019 -0500 |
| b |
| @@ -3,7 +3,7 @@ ENSG00000082175 GO:0000978 MF IDA ENSG00000141736 GO:0000165 BP TAS ENSG00000012048 GO:0000151 CC NAS -ENSG00000139618 GO:0000722 BP IEA +ENSG00000139618 GO:0000281 BP IDA ENSG00000129514 GO:0000122 BP IEA ENSG00000171862 GO:0000079 BP TAS ENSG00000141510 GO:0000122 BP IBA |