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comparison annotateMyIDs.xml @ 12:fe3ca740a485 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
author iuc
date Tue, 13 Sep 2022 09:25:40 +0000
parents 4f2967b27e67
children 133f36c29579
comparison
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11:4f2967b27e67 12:fe3ca740a485
1 <tool id="annotatemyids" name="annotateMyIDs" version="3.14.0+galaxy0"> 1 <tool id="annotatemyids" name="annotateMyIDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>annotate a generic set of identifiers</description> 2 <description>annotate a generic set of identifiers</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">annotatemyids</xref> 4 <xref type="bio.tools">annotatemyids</xref>
5 </xrefs> 5 </xrefs>
6 <macros>
7 <token name="@TOOL_VERSION@">3.14.0</token>
8 <token name="@VERSION_SUFFIX@">1</token>
9 </macros>
6 <requirements> 10 <requirements>
7 <requirement type="package" version="3.14.0">bioconductor-org.hs.eg.db</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.hs.eg.db</requirement>
8 <requirement type="package" version="3.14.0">bioconductor-org.mm.eg.db</requirement> 12 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.mm.eg.db</requirement>
9 <requirement type="package" version="3.14.0">bioconductor-org.dm.eg.db</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dm.eg.db</requirement>
10 <requirement type="package" version="3.14.0">bioconductor-org.dr.eg.db</requirement> 14 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dr.eg.db</requirement>
11 <requirement type="package" version="3.14.0">bioconductor-org.rn.eg.db</requirement> 15 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.rn.eg.db</requirement>
12 <requirement type="package" version="3.14.0">bioconductor-org.at.tair.db</requirement> 16 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.at.tair.db</requirement>
17 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.gg.eg.db</requirement>
13 </requirements> 18 </requirements>
14 <version_command><![CDATA[ 19 <version_command><![CDATA[
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: ") 20 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: ")
16 ]]></version_command> 21 ]]></version_command>
17 <command detect_errors="exit_code"><![CDATA[ 22 <command detect_errors="exit_code"><![CDATA[
53 suppressPackageStartupMessages(library(org.Rn.eg.db)) 58 suppressPackageStartupMessages(library(org.Rn.eg.db))
54 db <- org.Rn.eg.db 59 db <- org.Rn.eg.db
55 } else if (organism == "At"){ 60 } else if (organism == "At"){
56 suppressPackageStartupMessages(library(org.At.tair.db)) 61 suppressPackageStartupMessages(library(org.At.tair.db))
57 db <- org.At.tair.db 62 db <- org.At.tair.db
63 } else if (organism == "Gg"){
64 suppressPackageStartupMessages(library(org.Gg.eg.db))
65 db <- org.Gg.eg.db
58 } else { 66 } else {
59 cat(paste("Organism type not supported", organism)) 67 cat(paste("Organism type not supported", organism))
60 } 68 }
61 69
62 cols <- unlist(strsplit(output_cols, ",")) 70 cols <- unlist(strsplit(output_cols, ","))
78 <option value="Mm">Mouse</option> 86 <option value="Mm">Mouse</option>
79 <option value="Rn">Rat</option> 87 <option value="Rn">Rat</option>
80 <option value="Dm">Fruit fly</option> 88 <option value="Dm">Fruit fly</option>
81 <option value="Dr">Zebrafish</option> 89 <option value="Dr">Zebrafish</option>
82 <option value="At">Arabidopsis thaliana</option> 90 <option value="At">Arabidopsis thaliana</option>
91 <option value="Gg">Gallus gallus</option>
83 </param> 92 </param>
84 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file"> 93 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
85 <option value="ENSEMBL" selected="true">Ensembl Gene</option> 94 <option value="ENSEMBL" selected="true">Ensembl Gene</option>
86 <option value="ENSEMBLPROT">Ensembl Protein</option> 95 <option value="ENSEMBLPROT">Ensembl Protein</option>
87 <option value="ENSEMBLTRANS">Ensembl Transcript</option> 96 <option value="ENSEMBLTRANS">Ensembl Transcript</option>
155 <param name="id_type" value="SYMBOL"/> 164 <param name="id_type" value="SYMBOL"/>
156 <param name="organism" value="At"/> 165 <param name="organism" value="At"/>
157 <param name="output_cols" value="GO,ENTREZID" /> 166 <param name="output_cols" value="GO,ENTREZID" />
158 <output name="out_tab" file="out_arabidopsis.tab" /> 167 <output name="out_tab" file="out_arabidopsis.tab" />
159 </test> 168 </test>
169 <!-- Gallus gallus database -->
170 <test expect_num_outputs="1">
171 <param name="id_file" value="genelist_gallus.txt" ftype="tabular"/>
172 <param name="id_type" value="SYMBOL"/>
173 <param name="organism" value="Gg"/>
174 <param name="output_cols" value="GO,ENTREZID" />
175 <output name="out_tab" file="out_gallus.tab" />
176 </test>
160 </tests> 177 </tests>
161 <help><![CDATA[ 178 <help><![CDATA[
162 179
163 .. class:: infomark 180 .. class:: infomark
164 181