| Previous changeset 11:4f2967b27e67 (2022-07-01) Next changeset 13:133f36c29579 (2023-01-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707 |
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modified:
annotateMyIDs.xml |
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added:
test-data/genelist_gallus.txt test-data/out_gallus.tab |
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| diff -r 4f2967b27e67 -r fe3ca740a485 annotateMyIDs.xml --- a/annotateMyIDs.xml Fri Jul 01 12:24:49 2022 +0000 +++ b/annotateMyIDs.xml Tue Sep 13 09:25:40 2022 +0000 |
| [ |
| @@ -1,15 +1,20 @@ -<tool id="annotatemyids" name="annotateMyIDs" version="3.14.0+galaxy0"> +<tool id="annotatemyids" name="annotateMyIDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>annotate a generic set of identifiers</description> <xrefs> <xref type="bio.tools">annotatemyids</xref> </xrefs> + <macros> + <token name="@TOOL_VERSION@">3.14.0</token> + <token name="@VERSION_SUFFIX@">1</token> + </macros> <requirements> - <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> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dm.eg.db</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dr.eg.db</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.rn.eg.db</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.at.tair.db</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.gg.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: ")", 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: ") @@ -55,6 +60,9 @@ } else if (organism == "At"){ suppressPackageStartupMessages(library(org.At.tair.db)) db <- org.At.tair.db +} else if (organism == "Gg"){ + suppressPackageStartupMessages(library(org.Gg.eg.db)) + db <- org.Gg.eg.db } else { cat(paste("Organism type not supported", organism)) } @@ -80,6 +88,7 @@ <option value="Dm">Fruit fly</option> <option value="Dr">Zebrafish</option> <option value="At">Arabidopsis thaliana</option> + <option value="Gg">Gallus gallus</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> @@ -157,6 +166,14 @@ <param name="output_cols" value="GO,ENTREZID" /> <output name="out_tab" file="out_arabidopsis.tab" /> </test> + <!-- Gallus gallus database --> + <test expect_num_outputs="1"> + <param name="id_file" value="genelist_gallus.txt" ftype="tabular"/> + <param name="id_type" value="SYMBOL"/> + <param name="organism" value="Gg"/> + <param name="output_cols" value="GO,ENTREZID" /> + <output name="out_tab" file="out_gallus.tab" /> + </test> </tests> <help><![CDATA[ |
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| diff -r 4f2967b27e67 -r fe3ca740a485 test-data/genelist_gallus.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genelist_gallus.txt Tue Sep 13 09:25:40 2022 +0000 |
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| @@ -0,0 +1,4 @@ +TRIM15 +TENM2 +FZD10 +ADRA1B |
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| diff -r 4f2967b27e67 -r fe3ca740a485 test-data/out_gallus.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_gallus.tab Tue Sep 13 09:25:40 2022 +0000 |
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| @@ -0,0 +1,43 @@ +SYMBOL GO EVIDENCE ONTOLOGY ENTREZID +TRIM15 NA NA NA NA +TENM2 GO:0000122 IDA BP 373854 +TENM2 GO:0005102 ISS MF 373854 +TENM2 GO:0005509 IEA MF 373854 +TENM2 GO:0005634 IDA CC 373854 +TENM2 GO:0005783 IDA CC 373854 +TENM2 GO:0005794 IDA CC 373854 +TENM2 GO:0005886 IDA CC 373854 +TENM2 GO:0005887 IEA CC 373854 +TENM2 GO:0005911 ISS CC 373854 +TENM2 GO:0007157 IBA BP 373854 +TENM2 GO:0007157 ISS BP 373854 +TENM2 GO:0007411 ISS BP 373854 +TENM2 GO:0016605 IDA CC 373854 +TENM2 GO:0030054 IDA CC 373854 +TENM2 GO:0030175 IDA CC 373854 +TENM2 GO:0030425 IDA CC 373854 +TENM2 GO:0030426 IDA CC 373854 +TENM2 GO:0035584 ISS BP 373854 +TENM2 GO:0042803 IBA MF 373854 +TENM2 GO:0042803 ISS MF 373854 +TENM2 GO:0043005 IBA CC 373854 +TENM2 GO:0043005 ISS CC 373854 +TENM2 GO:0043197 ISS CC 373854 +TENM2 GO:0045202 ISS CC 373854 +TENM2 GO:0045211 ISS CC 373854 +TENM2 GO:0046982 IBA MF 373854 +TENM2 GO:0046982 ISS MF 373854 +TENM2 GO:0048666 IBA BP 373854 +TENM2 GO:0050839 IBA MF 373854 +TENM2 GO:0050839 ISS MF 373854 +TENM2 GO:0051491 IDA BP 373854 +TENM2 GO:0098609 IDA BP 373854 +FZD10 GO:0004930 IEA MF 373885 +FZD10 GO:0005886 IBA CC 373885 +FZD10 GO:0007186 IEA BP 373885 +FZD10 GO:0016021 IBA CC 373885 +FZD10 GO:0017147 IBA MF 373885 +FZD10 GO:0035567 IBA BP 373885 +FZD10 GO:0042813 IBA MF 373885 +FZD10 GO:0060070 IBA BP 373885 +ADRA1B NA NA NA 373890 |