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comparison annotateMyIDs.xml @ 11:4f2967b27e67 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
author iuc
date Fri, 01 Jul 2022 12:24:49 +0000
parents f29602ae449e
children fe3ca740a485
comparison
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10:f29602ae449e 11:4f2967b27e67
1 <tool id="annotatemyids" name="annotateMyIDs" version="3.12.0+galaxy1"> 1 <tool id="annotatemyids" name="annotateMyIDs" version="3.14.0+galaxy0">
2 <description>annotate a generic set of identifiers</description> 2 <description>annotate a generic set of identifiers</description>
3 <xrefs>
4 <xref type="bio.tools">annotatemyids</xref>
5 </xrefs>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="3.12.0">bioconductor-org.hs.eg.db</requirement> 7 <requirement type="package" version="3.14.0">bioconductor-org.hs.eg.db</requirement>
5 <requirement type="package" version="3.12.0">bioconductor-org.mm.eg.db</requirement> 8 <requirement type="package" version="3.14.0">bioconductor-org.mm.eg.db</requirement>
6 <requirement type="package" version="3.12.0">bioconductor-org.dm.eg.db</requirement> 9 <requirement type="package" version="3.14.0">bioconductor-org.dm.eg.db</requirement>
7 <requirement type="package" version="3.12.0">bioconductor-org.dr.eg.db</requirement> 10 <requirement type="package" version="3.14.0">bioconductor-org.dr.eg.db</requirement>
8 <requirement type="package" version="3.12.0">bioconductor-org.rn.eg.db</requirement> 11 <requirement type="package" version="3.14.0">bioconductor-org.rn.eg.db</requirement>
12 <requirement type="package" version="3.14.0">bioconductor-org.at.tair.db</requirement>
9 </requirements> 13 </requirements>
10 <version_command><![CDATA[ 14 <version_command><![CDATA[
11 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: ") 15 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: ")
12 ]]></version_command> 16 ]]></version_command>
13 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
46 suppressPackageStartupMessages(library(org.Dr.eg.db)) 50 suppressPackageStartupMessages(library(org.Dr.eg.db))
47 db <- org.Dr.eg.db 51 db <- org.Dr.eg.db
48 } else if (organism == "Rn"){ 52 } else if (organism == "Rn"){
49 suppressPackageStartupMessages(library(org.Rn.eg.db)) 53 suppressPackageStartupMessages(library(org.Rn.eg.db))
50 db <- org.Rn.eg.db 54 db <- org.Rn.eg.db
55 } else if (organism == "At"){
56 suppressPackageStartupMessages(library(org.At.tair.db))
57 db <- org.At.tair.db
51 } else { 58 } else {
52 cat(paste("Organism type not supported", organism)) 59 cat(paste("Organism type not supported", organism))
53 } 60 }
54 61
55 cols <- unlist(strsplit(output_cols, ",")) 62 cols <- unlist(strsplit(output_cols, ","))
70 <option value="Hs" selected="true">Human</option> 77 <option value="Hs" selected="true">Human</option>
71 <option value="Mm">Mouse</option> 78 <option value="Mm">Mouse</option>
72 <option value="Rn">Rat</option> 79 <option value="Rn">Rat</option>
73 <option value="Dm">Fruit fly</option> 80 <option value="Dm">Fruit fly</option>
74 <option value="Dr">Zebrafish</option> 81 <option value="Dr">Zebrafish</option>
82 <option value="At">Arabidopsis thaliana</option>
75 </param> 83 </param>
76 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file"> 84 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
77 <option value="ENSEMBL" selected="true">Ensembl Gene</option> 85 <option value="ENSEMBL" selected="true">Ensembl Gene</option>
78 <option value="ENSEMBLPROT">Ensembl Protein</option> 86 <option value="ENSEMBLPROT">Ensembl Protein</option>
79 <option value="ENSEMBLTRANS">Ensembl Transcript</option> 87 <option value="ENSEMBLTRANS">Ensembl Transcript</option>
139 <param name="organism" value="Hs"/> 147 <param name="organism" value="Hs"/>
140 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> 148 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
141 <param name="remove_dups" value="True" /> 149 <param name="remove_dups" value="True" />
142 <output name="out_tab" file="out_gokegg_dupsrem.tab" /> 150 <output name="out_tab" file="out_gokegg_dupsrem.tab" />
143 </test> 151 </test>
152 <!-- Arabidopsis database -->
153 <test expect_num_outputs="1">
154 <param name="id_file" value="genelist_arabidopsis.txt" ftype="tabular"/>
155 <param name="id_type" value="SYMBOL"/>
156 <param name="organism" value="At"/>
157 <param name="output_cols" value="GO,ENTREZID" />
158 <output name="out_tab" file="out_arabidopsis.tab" />
159 </test>
144 </tests> 160 </tests>
145 <help><![CDATA[ 161 <help><![CDATA[
146 162
147 .. class:: infomark 163 .. class:: infomark
148 164