| Previous changeset 1:2e1b256f732f (2018-01-03) Next changeset 3:1a125daea0d8 (2018-11-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab |
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modified:
annotateMyIDs.xml |
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added:
test-data/out_gokegg_dupsrem.tab |
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| diff -r 2e1b256f732f -r 9ab35a2245ce annotateMyIDs.xml --- a/annotateMyIDs.xml Wed Jan 03 16:01:27 2018 -0500 +++ b/annotateMyIDs.xml Sun Mar 11 05:17:23 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="annotatemyids" name="annotateMyIDs" version="3.5.0.0"> +<tool id="annotatemyids" name="annotateMyIDs" version="3.5.0.1"> <description>annotate a generic set of identifiers</description> <requirements> <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> @@ -7,7 +7,7 @@ <requirement type="package" version="3.5.0">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: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ") +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: ") ]]></version_command> <command detect_errors="exit_code"><![CDATA[ #if $rscriptOpt: @@ -27,6 +27,7 @@ organism <- "${organism}" output_cols <- "${output_cols}" file_has_header <- ${file_has_header} +remove_dups <- ${remove_dups} ids <- as.character(read.table('$id_file', header=file_has_header)[,1]) @@ -48,6 +49,11 @@ cols <- unlist(strsplit(output_cols, ",")) result <- select(db, keys=ids, keytype=id_type, columns=cols) + +if(remove_dups) { + result <- result[!duplicated(result$${id_type}),] +} + write.table(result, file='$out_tab', sep="\t", row.names=FALSE, quote=FALSE) ]]></configfile> @@ -87,6 +93,7 @@ <option value="ONTOLOGY">ONTOLOGY</option> <option value="PATH">KEGG</option> </param> + <param name="remove_dups" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Remove duplicates?" help="If this option is set to Yes, only the first occurrence of each input Gene ID will be kept. Default: No" /> <param name="rscriptOpt" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" /> </inputs> <outputs> @@ -118,7 +125,16 @@ <param name="id_type" value="ENSEMBL"/> <param name="organism" value="Hs"/> <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> - <output name="out_tab" file="out_gokegg.tab" compare="contains" /> + <output name="out_tab" file="out_gokegg.tab" /> + </test> + <!-- Ensure duplicate Gene ID removal works --> + <test expect_num_outputs="1"> + <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/> + <param name="id_type" value="ENSEMBL"/> + <param name="organism" value="Hs"/> + <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> + <param name="remove_dups" value="True" /> + <output name="out_tab" file="out_gokegg_dupsrem.tab" /> </test> </tests> <help><![CDATA[ |
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| diff -r 2e1b256f732f -r 9ab35a2245ce test-data/out_gokegg_dupsrem.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_gokegg_dupsrem.tab Sun Mar 11 05:17:23 2018 -0400 |
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| @@ -0,0 +1,9 @@ +ENSEMBL GO ONTOLOGY EVIDENCE +ENSG00000091831 GO:0000122 BP IMP +ENSG00000082175 GO:0000978 MF IDA +ENSG00000141736 GO:0000165 BP TAS +ENSG00000012048 GO:0000151 CC NAS +ENSG00000139618 GO:0000722 BP IEA +ENSG00000129514 GO:0000122 BP IEA +ENSG00000171862 GO:0000079 BP TAS +ENSG00000141510 GO:0000122 BP IBA |