Mercurial > repos > iuc > annotatemyids
comparison annotateMyIDs.xml @ 2:9ab35a2245ce draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
author | iuc |
---|---|
date | Sun, 11 Mar 2018 05:17:23 -0400 |
parents | 2e1b256f732f |
children | 1a125daea0d8 |
comparison
equal
deleted
inserted
replaced
1:2e1b256f732f | 2:9ab35a2245ce |
---|---|
1 <tool id="annotatemyids" name="annotateMyIDs" version="3.5.0.0"> | 1 <tool id="annotatemyids" name="annotateMyIDs" version="3.5.0.1"> |
2 <description>annotate a generic set of identifiers</description> | 2 <description>annotate a generic set of identifiers</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> | 4 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> |
5 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> | 5 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> |
6 <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement> | 6 <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement> |
7 <requirement type="package" version="3.5.0">bioconductor-org.dr.eg.db</requirement> | 7 <requirement type="package" version="3.5.0">bioconductor-org.dr.eg.db</requirement> |
8 </requirements> | 8 </requirements> |
9 <version_command><![CDATA[ | 9 <version_command><![CDATA[ |
10 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: ") | 10 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: ") |
11 ]]></version_command> | 11 ]]></version_command> |
12 <command detect_errors="exit_code"><![CDATA[ | 12 <command detect_errors="exit_code"><![CDATA[ |
13 #if $rscriptOpt: | 13 #if $rscriptOpt: |
14 cp '${annotatemyids_script}' '${out_rscript}' && | 14 cp '${annotatemyids_script}' '${out_rscript}' && |
15 #end if | 15 #end if |
25 | 25 |
26 id_type <- "${id_type}" | 26 id_type <- "${id_type}" |
27 organism <- "${organism}" | 27 organism <- "${organism}" |
28 output_cols <- "${output_cols}" | 28 output_cols <- "${output_cols}" |
29 file_has_header <- ${file_has_header} | 29 file_has_header <- ${file_has_header} |
30 remove_dups <- ${remove_dups} | |
30 | 31 |
31 ids <- as.character(read.table('$id_file', header=file_has_header)[,1]) | 32 ids <- as.character(read.table('$id_file', header=file_has_header)[,1]) |
32 | 33 |
33 if(organism == "Hs"){ | 34 if(organism == "Hs"){ |
34 suppressPackageStartupMessages(library(org.Hs.eg.db)) | 35 suppressPackageStartupMessages(library(org.Hs.eg.db)) |
46 cat(paste("Organism type not supported", organism)) | 47 cat(paste("Organism type not supported", organism)) |
47 } | 48 } |
48 | 49 |
49 cols <- unlist(strsplit(output_cols, ",")) | 50 cols <- unlist(strsplit(output_cols, ",")) |
50 result <- select(db, keys=ids, keytype=id_type, columns=cols) | 51 result <- select(db, keys=ids, keytype=id_type, columns=cols) |
52 | |
53 if(remove_dups) { | |
54 result <- result[!duplicated(result$${id_type}),] | |
55 } | |
56 | |
51 write.table(result, file='$out_tab', sep="\t", row.names=FALSE, quote=FALSE) | 57 write.table(result, file='$out_tab', sep="\t", row.names=FALSE, quote=FALSE) |
52 | 58 |
53 ]]></configfile> | 59 ]]></configfile> |
54 </configfiles> | 60 </configfiles> |
55 <inputs> | 61 <inputs> |
85 <option value="REFSEQ">REFSEQ</option> | 91 <option value="REFSEQ">REFSEQ</option> |
86 <option value="GO">GO</option> | 92 <option value="GO">GO</option> |
87 <option value="ONTOLOGY">ONTOLOGY</option> | 93 <option value="ONTOLOGY">ONTOLOGY</option> |
88 <option value="PATH">KEGG</option> | 94 <option value="PATH">KEGG</option> |
89 </param> | 95 </param> |
96 <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" /> | |
90 <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" /> | 97 <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" /> |
91 </inputs> | 98 </inputs> |
92 <outputs> | 99 <outputs> |
93 <data name="out_tab" format="tabular" from_work_dir="*.tab" label="${tool.name} on ${on_string}: Annotated IDs" /> | 100 <data name="out_tab" format="tabular" from_work_dir="*.tab" label="${tool.name} on ${on_string}: Annotated IDs" /> |
94 <data name="out_rscript" format="txt" from_work_dir="*.txt" label="${tool.name} on ${on_string}: Rscript"> | 101 <data name="out_rscript" format="txt" from_work_dir="*.txt" label="${tool.name} on ${on_string}: Rscript"> |
116 <test expect_num_outputs="1"> | 123 <test expect_num_outputs="1"> |
117 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/> | 124 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/> |
118 <param name="id_type" value="ENSEMBL"/> | 125 <param name="id_type" value="ENSEMBL"/> |
119 <param name="organism" value="Hs"/> | 126 <param name="organism" value="Hs"/> |
120 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> | 127 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> |
121 <output name="out_tab" file="out_gokegg.tab" compare="contains" /> | 128 <output name="out_tab" file="out_gokegg.tab" /> |
129 </test> | |
130 <!-- Ensure duplicate Gene ID removal works --> | |
131 <test expect_num_outputs="1"> | |
132 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/> | |
133 <param name="id_type" value="ENSEMBL"/> | |
134 <param name="organism" value="Hs"/> | |
135 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> | |
136 <param name="remove_dups" value="True" /> | |
137 <output name="out_tab" file="out_gokegg_dupsrem.tab" /> | |
122 </test> | 138 </test> |
123 </tests> | 139 </tests> |
124 <help><![CDATA[ | 140 <help><![CDATA[ |
125 | 141 |
126 .. class:: infomark | 142 .. class:: infomark |