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annotate annotateMyIDs.xml @ 0:af97bb1b9435 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
author iuc
date Wed, 03 Jan 2018 15:24:55 -0500
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children 11a9c9573c07
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af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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1 <tool id="annotateMyIDs" name="annotateMyIDs" version="3.5.0.0">
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2 <description>annotate a generic set of identifiers</description>
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3 <requirements>
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4 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
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5 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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6 <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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7 <requirement type="package" version="3.5.0">bioconductor-org.dr.eg.db</requirement>
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8 </requirements>
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9 <version_command><![CDATA[
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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: ")
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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11 ]]></version_command>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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12 <command detect_errors="exit_code"><![CDATA[
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13 #if $rscriptOpt:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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14 cp '${annotatemyids_script}' '${out_rscript}' &&
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15 #end if
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16 Rscript '${annotatemyids_script}'
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17 ]]>
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18 </command>
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19 <configfiles>
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20 <configfile name="annotatemyids_script"><![CDATA[
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21 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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22
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23 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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24 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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25
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26 id_type <- "${id_type}"
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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27 organism <- "${organism}"
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28 output_cols <- "${output_cols}"
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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29 file_has_header <- ${file_has_header}
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30
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31 ids <- as.character(read.table('$id_file', header=file_has_header)[,1])
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32
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33 if(organism == "Hs"){
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34 suppressPackageStartupMessages(library(org.Hs.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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35 db <- org.Hs.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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36 } else if (organism == "Mm"){
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37 suppressPackageStartupMessages(library(org.Mm.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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38 db <- org.Mm.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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39 } else if (organism == "Dm"){
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40 suppressPackageStartupMessages(library(org.Dm.eg.db))
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41 db <- org.Dm.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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42 } else if (organism == "Dr"){
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43 suppressPackageStartupMessages(library(org.Dr.eg.db))
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44 db <- org.Dr.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
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45 } else {
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46 cat(paste("Organism type not supported", organism))
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47 }
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48
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49 cols <- unlist(strsplit(output_cols, ","))
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50 result <- select(db, keys=ids, keytype=id_type, columns=cols)
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51 write.table(result, file='$out_tab', sep="\t", row.names=FALSE, quote=FALSE)
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52
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53 ]]></configfile>
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54 </configfiles>
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55 <inputs>
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56 <param name="id_file" type="data" format="tabular" label="File with IDs" help="A tabular file with the first column containing one of the supported types of identifier, see Help below." />
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57 <param name="file_has_header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="File has header?" help="If this option is set to Yes, the tool will assume that the input file has a column header in the first row and the identifers commence on the second line. Default: No" />
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58 <param name="organism" type="select" label="Organism" help="Select the organism the identifiers are from">
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59 <option value="Hs" selected="true">Human</option>
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60 <option value="Mm">Mouse</option>
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61 <option value="Dm">Fruit fly</option>
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62 <option value="Dr">Zebrafish</option>
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63 </param>
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64 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
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65 <option value="ENSEMBL" selected="true">Ensembl Gene</option>
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66 <option value="ENSEMBLPROT">Ensembl Protein</option>
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67 <option value="ENSEMBLTRANS">Ensembl Transcript</option>
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68 <option value="ENTREZID">Entrez</option>
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69 <option value="FLYBASE">FlyBase</option>
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70 <option value="GO">GO</option>
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71 <option value="PATH">KEGG</option>
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72 <option value="MGI">MGI</option>
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73 <option value="REFSEQ">RefSeq</option>
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74 <option value="SYMBOL">Gene Symbol</option>
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75 <option value="ZFIN">Zfin</option>
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76 </param>
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77 <param name="output_cols" type="select" multiple="True" display="checkboxes" label="Output columns" help="Choose the columns you want in the output table. Note that selecting some columns such as GO or KEGG could make the table very large as some genes may be associated with many terms. Default: ENSEMBL, ENTREZID, SYMBOL, GENENAME">
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78 <option value="ALIAS">ALIAS</option>
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79 <option value="DESCRIPTION">DESCRIPTION</option>
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80 <option value="ENSEMBL" selected="True">ENSEMBL</option>
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81 <option value="ENTREZID" selected="True">ENTREZID</option>
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82 <option value="EVIDENCE">EVIDENCE</option>
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83 <option value="SYMBOL" selected="True">SYMBOL</option>
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84 <option value="GENENAME" selected="True">GENENAME</option>
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85 <option value="REFSEQ">REFSEQ</option>
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86 <option value="GO">GO</option>
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87 <option value="ONTOLOGY">ONTOLOGY</option>
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88 <option value="PATH">KEGG</option>
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89 </param>
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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" />
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91 </inputs>
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92 <outputs>
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93 <data name="out_tab" format="tabular" from_work_dir="*.tab" label="${tool.name} on ${on_string}: Annotated IDs" />
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94 <data name="out_rscript" format="txt" from_work_dir="*.txt" label="${tool.name} on ${on_string}: Rscript">
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95 <filter>rscriptOpt is True</filter>
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96 </data>
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97 </outputs>
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98 <tests>
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99 <!-- Ensure output table works -->
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100 <test expect_num_outputs="1">
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101 <param name="id_file" value="genelist.txt" ftype="tabular"/>
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102 <param name="id_type" value="SYMBOL"/>
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103 <param name="organism" value="Hs"/>
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104 <output name="out_tab" file="out.tab" />
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105 </test>
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106 <!-- Ensure Ensembl IDs input and Rscript output work -->
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107 <test expect_num_outputs="2">
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108 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
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109 <param name="id_type" value="ENSEMBL"/>
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110 <param name="organism" value="Hs"/>
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111 <param name="rscriptOpt" value="True" />
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112 <output name="out_tab" file="out_ensembl.tab" />
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113 <output name="out_rscript" file="out_rscript.txt" compare="sim_size" />
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114 </test>
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115 <!-- Ensure GO and KEGG output work -->
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116 <test expect_num_outputs="1">
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117 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
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118 <param name="id_type" value="ENSEMBL"/>
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119 <param name="organism" value="Hs"/>
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120 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
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121 <output name="out_tab" file="out_gokegg.tab" compare="contains" />
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122 </test>
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123 </tests>
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124 <help><![CDATA[
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125
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126 .. class:: infomark
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127
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128 **What it does**
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129
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130 This tool can get annotation for a generic set of IDs, using the Bioconductor_ annotation data packages. Supported organisms are human, mouse, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here_.
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131
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132 Examples of what this tool can be used for are:
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133
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134 * adding gene names to IDs
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135 * mapping between IDs e.g. Entrez, Ensembl, Symbols
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136 * adding GO and KEGG identifiers
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137
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138 .. _Bioconductor: https://www.bioconductor.org/
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139 .. _here: http://bioconductor.org/packages/release/data/annotation/manuals/org.Hs.eg.db/man/org.Hs.eg.db.pdf
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140
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141 -----
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142
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143 **Inputs**
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144
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145 A tab-delimited file with identifiers in the first column. If the file contains a header row, select the file has a header option in the tool form above.
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146
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147 Example:
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148
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149 =============== =======================
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150 **GeneID** *Additional Columns...*
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151 --------------- -----------------------
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152 ENSG00000091831
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153 ENSG00000082175
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154 ENSG00000141736
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155 ENSG00000012048
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156 ENSG00000139618
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157 ENSG00000129514
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158 ENSG00000171862
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159 ENSG00000141510
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160 =============== =======================
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161
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162 ID types supported for input are:
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163
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164 * **ENSEMBL**: Ensembl gene IDs
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165 * **ENSEMBLPROT**: Ensembl protein IDs
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166 * **ENSEMBLTRANS**: Ensembl transcript IDs
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167 * **ENTREZID**: Entrez gene Identifiers
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168 * **FLYBASE**: FlyBase accession numbers
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169 * **GO**: GO Identifiers
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170 * **MGI**: Jackson Laboratory MGI gene accession numbers
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171 * **PATH**: KEGG Pathway Identifiers
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172 * **REFSEQ**: Refseq Identifiers
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173 * **SYMBOL**: The official gene symbol
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174 * **ZFIN**: Zfin accession numbers
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175
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176 .. class:: warningmark
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177
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178 This tool uses the ``select`` function from the Bioconductor AnnotationDBi_ package. Note that if you request columns that have multiple matches for your IDs, select will return *one row in the output for each possible match*. This has the effect that if you request multiple columns and some of them have a many-to-one relationship to the IDs, things will continue to multiply accordingly. So it's not a good idea to request a large number of columns unless you know what you are asking for should have a one-to-one relationship with the initial set of IDs. In general, if you need to retrieve a column like **GO** or **KEGG**, that has a many-to-one relationship to the original IDs, it is most useful to extract that separately.
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179
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180 .. _AnnotationDBi: https://www.bioconductor.org/packages/devel/bioc/manuals/AnnotationDbi/man/AnnotationDbi.pdf
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181
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182 -----
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183
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184 **Outputs**
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185
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186 If the input IDs are Ensembl, the default output will be similar to below, containing four columns. Other columns, such as GO and KEGG terms, can be selected above to be added as additional columns.
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187
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188 Example:
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189
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190 =============== ============ ========== =================================
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191 **ENSEMBL** **ENTREZID** **SYMBOL** **GENENAME**
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192 --------------- ------------ ---------- ---------------------------------
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193 ENSG00000091831 2099 ESR1 estrogen receptor 1
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194 ENSG00000082175 5241 PGR progesterone receptor
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195 ENSG00000141736 2064 ERBB2 erb-b2 receptor tyrosine kinase 2
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196 ENSG00000012048 672 BRCA1 breast cancer 1
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197 ENSG00000139618 675 BRCA2 breast cancer 2
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198 ENSG00000129514 3169 FOXA1 forkhead box A1
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199 ENSG00000171862 5728 PTEN phosphatase and tensin homolog
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200 ENSG00000141510 7157 TP53 tumor protein p53
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201 =============== ============ ========== =================================
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202
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203 Columns available for output include many of the ID columns already described under Inputs above and also:
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204
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205 * **ALIAS**: Commonly used gene symbols
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206 * **DESCRIPTION**: The description of the associated gene
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207 * **EVIDENCE**: Evidence codes for GO associations with a gene of interest
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208 * **GENENAME**: The full gene name
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209 * **ONTOLOGY**: For GO Identifiers, which Gene Ontology (BP, CC, or MF)
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210
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211 ]]></help>
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212 <citations>
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213 <citation type="bibtex">
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214 @unpublished{None,
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215 author = {Mark Dunning},
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216 title = {annotateMyIDs},
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217 year = {2017},
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218 eprint = {None},
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219 url = {}
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220 }</citation>
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221 </citations>
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222 </tool>