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1 <tool name="TermMapperTool" id="TermMapperTool1" version="0.0.2">
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2 <description>use cross-reference lookup tables to annotate results</description>
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3 <!--
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4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
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5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
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6 -->
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7 <!-- similar to "join two datasets" tool http://galaxy.wur.nl/galaxy_production/root?tool_id=join1
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8 but this one is probably having more powerful features like supporting multiple ';' codes in key fields
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9 and the feature in termColName(s) supporting direct hierarchy like annotation -->
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10 <command interpreter="java -jar ">
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11 TermMapperTool.jar
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12 -inputFileName $inputFileName
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13 -inputIdColumnName "$inputIdColumnName"
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14 #if $inputIdCol.inputIdHasPrefix == True
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15 -inputIdPrefix "$inputIdCol.inputIdPrefix"
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16 #end if
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17
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18 -mappingFileName $mappingFileName
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19 -mappingFileIdColName "$mappingFileIdColName"
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20
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21 #if $mappingIdCol.mappingIdHasPrefix == True
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22 -mappingIdPrefix "$mappingIdCol.mappingIdPrefix"
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23 #end if
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24
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25 -mappingFileTermColName "$mappingFileTermColName"
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26
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27 -outputFileName $outputFileName
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28
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29 #if $genObservations.genObservationsFile == True
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30 -outputObservationsFileName $outputObservationsFileName
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31 -quantifColumn "$genObservations.quantifColumn"
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32 -multipleMappingSolution $genObservations.multipleMappingSolution
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33 -filterZeros $genObservations.filterZeros
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34 #end if
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35
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36 -mappedTermsColName $mappedTermsColName
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37 -numberOfHeaderLines $numberOfHeaderLines
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38
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39 -htmlReportFile $htmlReportFile
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40 -htmlReportFilesPath $htmlReportFile.files_path
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41
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42 </command>
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43
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44 <inputs>
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45
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46 <param name="inputFileName" type="data" format="tabular,csv,txt" label="Target file (TSV/CSV)" />
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47
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48 <param name="inputIdColumnName" type="text" size="50" value="" label="ID column name"
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49 help="Name of the column containing the identification codes (in the given input file)"/>
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50
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51 <conditional name="inputIdCol">
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52 <param name="inputIdHasPrefix" type="boolean" truevalue="Yes" falsevalue="No" checked="false"
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53 label="ID values have a prefix"/>
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54 <when value="Yes">
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55 <param name="inputIdPrefix" type="text" size="50" value="" label="Prefix in ID column"
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56 help="Fill in if any prefix is found in the ID column values (e.g. in some
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57 files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this
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58 example one would fill in 'lipidmaps:' as prefix)"/>
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59 </when>
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60 <when value="No">
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61 </when>
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62 </conditional>
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63
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64 <!-- =================== cross-reference part ============== -->
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65 <param name="mappingFileName" type="data" format="tabular,csv" label="Lookup table (TSV/CSV)" help="Simple mapping file between the coding scheme used to another scheme"/>
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66 <param name="numberOfHeaderLines" type="select" label="Number of header lines in mapping file"
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67 help="If this is '0', use the column numbers starting from 1 as the 'names' in the paramters below.">
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68 <option value="0" >0</option>
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69 <option value="1" selected="true">1</option>
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70 </param>
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71
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72
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73 <param name="mappingFileIdColName" type="text" size="50" value="" label="ID column name or number (in lookup table)" help="Name (or number) of the ID column for the lookup"/>
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74
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75 <conditional name="mappingIdCol">
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76 <param name="mappingIdHasPrefix" type="boolean" truevalue="Yes" falsevalue="No" checked="false"
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77 label="ID values have a prefix"/>
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78 <when value="Yes">
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79 <param name="mappingIdPrefix" type="text" size="50" value="" label="Prefix in ID column"
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80 help="Fill in if any prefix is found in the ID column values (e.g. in some
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81 files the value is preceded by a fixed value like for example 'lipidmaps:LMFA00000007' instead of just 'LMFA00000007' - in this
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82 example one would fill in 'lipidmaps:' as prefix)"/>
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83 </when>
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84 <when value="No">
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85 </when>
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86 </conditional>
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87
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88 <param name="mappingFileTermColName" type="text" size="50" value="" label="Term column name(s) or number(s)"
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89 help="Name(s) or number(s) of the column(s) containing the term(s) in the lookup table (and which will be transfered to the target file based on ID match in 'ID column name').
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90 For using multiple term column names, set the names separated by comma (,).
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91 If multiple columns are specified, the algorithm will look for an annotation in the first one, if none
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92 found it will try the second one, and so forth. "/>
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93
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94
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95 <param name="mappedTermsColName" type="text" size="50" value="Mapped terms" label="Name to give to the new column"
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96 help="Name to give to the new column that will be added to the target file. This new column is the one
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97 that will contain the respectively mapped terms."/>
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98
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99 <conditional name="genObservations">
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100 <param name="genObservationsFile" type="boolean" truevalue="Yes" falsevalue="No" checked="false"
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101 label="Generate also observations file"/>
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102 <when value="Yes">
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103 <param name="quantifColumn" type="text" size="50" value=""
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104 label="(Optional) Values column name"
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105 help="Name of the column containing the quantification values (in the given input file)"/>
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106 <param name="multipleMappingSolution" type="select"
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107 label="(when using values column above) What to do when multiple items map to the same term"
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108 help="When e.g. two Uniprot codes map to the same KEGG code, which quantification value to use">
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109 <option value="not" selected="true">Do nothing, leave as is</option>
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110 <option value="max" >Use max value</option>
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111 <option value="min">Use min value</option>
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112 <option value="avg">Use avg value</option>
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113 </param>
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114 <param name="filterZeros" type="boolean" checked="false"
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115 label="Filter zeros"
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116 help="Filter out the items that have quantification value = 0"/>
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117 </when>
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118 <when value="No">
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119 </when>
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120 </conditional>
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121
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122
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123 </inputs>
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124 <outputs>
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125 #if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__):
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126 <data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data>
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127 #else:
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128 <data name="outputFileName" format="csv" label="${tool.name} on ${on_string}: annotated file " ></data>
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129 #end if
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130 #if $genObservations.genObservationsFile == True :
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131 <data name="outputObservationsFileName" format="tabular" label="${tool.name} on ${on_string}: term observations file (TSV)"></data>
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132 #end if
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133 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"/>
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134 </outputs>
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135 <tests>
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136 <!-- find out how to use -->
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137 <test>
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138 </test>
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139 </tests>
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140 <help>
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141
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142 .. class:: infomark
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143
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144
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145 This tool is responsible for annotating the given target file
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146 with the terms given in a lookup table. This lookup table maps the items found in the target file
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147 (e.g. protein identifications coded in common protein coding formats such as UniProt )
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148 to their respective terms (e.g. GO terms). It enables users to use the cross-reference
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149 information now available from different repositories (like uniprot and KEGG - see for example
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150 http://www.uniprot.org/taxonomy/ or http://www.genome.jp/linkdb/ )
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151 to map their data to other useful coding schemes or to ontologies and functional annotations.
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152
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153 .. class:: infomark
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154
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155 **NB:** Currently the tool will do "smart parsing" of hierarchy based fields in the target file ID column.
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156 This means that if the colum contains a ".", the trailing part of the ID after the "." is ignored if the full
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157 ID does not get a match in the lookup table while the part before the "." does.
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158
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159 .. class:: infomark
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160
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161 Examples of usage:
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162
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163 annotate protein identifications with Gene Ontology[GO] terms
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164
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165 annotate metabolite CAS identifications with chebi codes
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166
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167 add KEGG gene codes to a file containing UNIPROT codes
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168
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169 add KEGG compound codes to a file containing chebi codes
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170
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171 etc
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172
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173 As an example for transcripts and proteins, users can check http://www.uniprot.org/taxonomy/ to
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174 see if their organism has been mapped to GO terms by Uniprot. For example the link
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175 http://www.uniprot.org/uniprot/?query=taxonomy:2850 will show the Uniprot repository and cross-references
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176 for the taxonomy 2850.
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177 When the organism being studied is not available, then other strategies
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178 could be tried (like Blast2GO for example).
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179
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180 Despite the specific examples above, this class is generic and can be used to map any
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181 values to new terms according to a given lookup table.
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182
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183 .. class:: infomark
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184
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185 *Omics cross-reference resources on the web:*
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186
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187 LinkDB: http://www.genome.jp/linkdb/
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188
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189 *Ready to use metabolomics links:*
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190
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191 http://rest.genome.jp/link/compound/chebi
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192
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193 http://rest.genome.jp/link/compound/lipidmaps
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194
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195 http://rest.genome.jp/link/compound/lipidbank
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196
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197 http://rest.genome.jp/link/compound/hmdb
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198
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199
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200 *Ready to use proteomics links:*
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201
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202 http://rest.genome.jp/link/uniprot/pti (Phaeodactylum Tricornutum)
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203 http://rest.genome.jp/link/pti/uniprot
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204
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205 http://rest.genome.jp/link/uniprot/hsa (Homo Sapiens)
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206
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207 (for organism code list see: )
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208
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209
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210 Uniprot to GO
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211
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212 http://www.uniprot.org/taxonomy/
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213
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214 http://www.uniprot.org/uniprot/?sort=&desc=&query=proteome:UP000000759&fil=&format=tab&force=yes&columns=id,go-id (Phaeodactylum Tricornutum)
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215
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216
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217 -----
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218
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219 **Output**
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220
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221 This method will read in the given input file and for each line it will add a new column
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222 containing the terms found for the ID in that line. So the output file is the same as the
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223 input file + extra terms column (separated by ; ).
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224
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225 -----
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226
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227 **Link to ontology viewer**
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228
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229 A second summarized "terms observations" file can also be generated.
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230 In case the terms are ontology terms, this file can be used for visualizing the results
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231 in the ontology viewer "OntologyAndObservationsViewer".
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232
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233 </help>
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234 </tool>
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