Mercurial > repos > iuc > annotatemyids
diff annotateMyIDs.xml @ 11:344471c33167 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
| author | iuc |
|---|---|
| date | Fri, 01 Jul 2022 12:24:15 +0000 |
| parents | 40e7cdca3e8c |
| children | 6feec02cf814 |
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--- a/annotateMyIDs.xml Fri Jul 09 14:19:34 2021 +0000 +++ b/annotateMyIDs.xml Fri Jul 01 12:24:15 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[