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comparison annotateMyIDs.xml @ 15:2790d367cfbc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
author iuc
date Tue, 29 Aug 2023 22:44:11 +0000
parents dec0e9dbe336
children
comparison
equal deleted inserted replaced
14:dec0e9dbe336 15:2790d367cfbc
1 <tool id="annotatemyids" name="annotateMyIDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 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 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">3.17.0</token> 4 <token name="@TOOL_VERSION@">3.17.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">annotatemyids</xref> 8 <xref type="bio.tools">annotatemyids</xref>
9 </xrefs> 9 </xrefs>
10 <requirements> 10 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dm.eg.db</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dm.eg.db</requirement>
14 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dr.eg.db</requirement> 14 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dr.eg.db</requirement>
15 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.rn.eg.db</requirement> 15 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.rn.eg.db</requirement>
16 <requirement type="package" version="@TOOL_VERSION@">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> 17 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.gg.eg.db</requirement>
18 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.bt.eg.db</requirement>
18 </requirements> 19 </requirements>
19 <version_command><![CDATA[ 20 <version_command><![CDATA[
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: ") 21 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: ")", org.Bt.eg.db version" $(R --vanilla --slave -e "library(org.Bt.eg.db); cat(sessionInfo()\$otherPkgs\$org.Bt.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
21 ]]></version_command> 22 ]]></version_command>
22 <command detect_errors="exit_code"><![CDATA[ 23 <command detect_errors="exit_code"><![CDATA[
23 #if $rscriptOpt: 24 #if $rscriptOpt:
24 cp '${annotatemyids_script}' '${out_rscript}' && 25 cp '${annotatemyids_script}' '${out_rscript}' &&
25 #end if 26 #end if
61 suppressPackageStartupMessages(library(org.At.tair.db)) 62 suppressPackageStartupMessages(library(org.At.tair.db))
62 db <- org.At.tair.db 63 db <- org.At.tair.db
63 } else if (organism == "Gg"){ 64 } else if (organism == "Gg"){
64 suppressPackageStartupMessages(library(org.Gg.eg.db)) 65 suppressPackageStartupMessages(library(org.Gg.eg.db))
65 db <- org.Gg.eg.db 66 db <- org.Gg.eg.db
67 } else if (organism == "Bt"){
68 suppressPackageStartupMessages(library(org.Bt.eg.db))
69 db <- org.Bt.eg.db
66 } else { 70 } else {
67 cat(paste("Organism type not supported", organism)) 71 cat(paste("Organism type not supported", organism))
68 } 72 }
69 73
70 cols <- unlist(strsplit(output_cols, ",")) 74 cols <- unlist(strsplit(output_cols, ","))
87 <option value="Rn">Rat</option> 91 <option value="Rn">Rat</option>
88 <option value="Dm">Fruit fly</option> 92 <option value="Dm">Fruit fly</option>
89 <option value="Dr">Zebrafish</option> 93 <option value="Dr">Zebrafish</option>
90 <option value="At">Arabidopsis thaliana</option> 94 <option value="At">Arabidopsis thaliana</option>
91 <option value="Gg">Gallus gallus</option> 95 <option value="Gg">Gallus gallus</option>
96 <option value="Bt">Bos taurus</option>
92 </param> 97 </param>
93 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file"> 98 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
94 <option value="ENSEMBL" selected="true">Ensembl Gene</option> 99 <option value="ENSEMBL" selected="true">Ensembl Gene</option>
95 <option value="ENSEMBLPROT">Ensembl Protein</option> 100 <option value="ENSEMBLPROT">Ensembl Protein</option>
96 <option value="ENSEMBLTRANS">Ensembl Transcript</option> 101 <option value="ENSEMBLTRANS">Ensembl Transcript</option>
196 <has_n_lines min="40"/> 201 <has_n_lines min="40"/>
197 <has_text_matching expression="TENM2" min="20"/> 202 <has_text_matching expression="TENM2" min="20"/>
198 </assert_contents> 203 </assert_contents>
199 </output> 204 </output>
200 </test> 205 </test>
206 <!-- Bos taurus database -->
207 <test expect_num_outputs="1">
208 <param name="id_file" value="genelist.txt" ftype="tabular"/>
209 <param name="id_type" value="SYMBOL"/>
210 <param name="organism" value="Bt"/>
211 <param name="output_cols" value="ENSEMBL" />
212 <output name="out_tab">
213 <assert_contents>
214 <has_n_columns n="2"/>
215 <has_n_lines min="9"/>
216 <has_text_matching expression="ENSBTAG00000007159"/>
217 <has_text_matching expression="ENSBTAG00000009498"/>
218 </assert_contents>
219 </output>
220 </test>
201 </tests> 221 </tests>
202 <help><![CDATA[ 222 <help><![CDATA[
203 223
204 .. class:: infomark 224 .. class:: infomark
205 225