Mercurial > repos > pieterlukasse > primo_multiomics

comparison term_mapper.xml @ 9:89264646e458

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improvements release
author pieter.lukasse@wur.nl
date Sat, 28 Mar 2015 14:28:45 +0100
parents 97e10319d86f
children
comparison
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8:97e10319d86f 9:89264646e458
27 -outputFileName $outputFileName 27 -outputFileName $outputFileName
28 28
29 #if $genObservations.genObservationsFile == True 29 #if $genObservations.genObservationsFile == True
30 -outputObservationsFileName $outputObservationsFileName 30 -outputObservationsFileName $outputObservationsFileName
31 -quantifColumn "$genObservations.quantifColumn" 31 -quantifColumn "$genObservations.quantifColumn"
32 -multipleMappingSolution $genObservations.multipleMappingSolution
33 -filterZeros $genObservations.filterZeros
32 #end if 34 #end if
33 35
34 -mappedTermsColName $mappedTermsColName 36 -mappedTermsColName $mappedTermsColName
35 -numberOfHeaderLines $numberOfHeaderLines 37 -numberOfHeaderLines $numberOfHeaderLines
38
39 -htmlReportFile $htmlReportFile
40 -htmlReportFilesPath $htmlReportFile.files_path
36 41
37 </command> 42 </command>
38 43
39 <inputs> 44 <inputs>
40 45
41 <param name="inputFileName" type="data" format="tabular,csv" label="Target file (TSV/CSV)" /> 46 <param name="inputFileName" type="data" format="tabular,csv,txt" label="Target file (TSV/CSV)" />
42 47
43 <param name="inputIdColumnName" type="text" size="50" value="" label="ID column name" 48 <param name="inputIdColumnName" type="text" size="50" value="" label="ID column name"
44 help="Name of the column containing the identification codes (in the given input file)"/> 49 help="Name of the column containing the identification codes (in the given input file)"/>
45 50
46 <conditional name="inputIdCol"> 51 <conditional name="inputIdCol">
63 <option value="0" >0</option> 68 <option value="0" >0</option>
64 <option value="1" selected="true">1</option> 69 <option value="1" selected="true">1</option>
65 </param> 70 </param>
66 71
67 72
68 <param name="mappingFileIdColName" type="text" size="50" value="" label="ID column name (in lookup table)" help="Name of the ID column for the lookup"/> 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"/>
69 74
70 <conditional name="mappingIdCol"> 75 <conditional name="mappingIdCol">
71 <param name="mappingIdHasPrefix" type="boolean" truevalue="Yes" falsevalue="No" checked="false" 76 <param name="mappingIdHasPrefix" type="boolean" truevalue="Yes" falsevalue="No" checked="false"
72 label="ID values have a prefix"/> 77 label="ID values have a prefix"/>
73 <when value="Yes"> 78 <when value="Yes">
85 For using multiple term column names, set the names separated by comma (,). 90 For using multiple term column names, set the names separated by comma (,).
86 If multiple columns are specified, the algorithm will look for an annotation in the first one, if none 91 If multiple columns are specified, the algorithm will look for an annotation in the first one, if none
87 found it will try the second one, and so forth. "/> 92 found it will try the second one, and so forth. "/>
88 93
89 94
90 <param name="mappedTermsColName" type="text" size="50" value="Mapped terms" label="Name to give to the new column:" 95 <param name="mappedTermsColName" type="text" size="50" value="Mapped terms" label="Name to give to the new column"
91 help="Name to give to the new column that will be added to the target file. This new column is the one 96 help="Name to give to the new column that will be added to the target file. This new column is the one
92 that will contain the respectively mapped terms."/> 97 that will contain the respectively mapped terms."/>
93 98
94 <conditional name="genObservations"> 99 <conditional name="genObservations">
95 <param name="genObservationsFile" type="boolean" truevalue="Yes" falsevalue="No" checked="false" 100 <param name="genObservationsFile" type="boolean" truevalue="Yes" falsevalue="No" checked="false"
96 label="Generate also observations file"/> 101 label="Generate also observations file"/>
97 <when value="Yes"> 102 <when value="Yes">
98 <param name="quantifColumn" type="text" size="50" value="" 103 <param name="quantifColumn" type="text" size="50" value=""
99 label="(Optional) Values column name" 104 label="(Optional) Values column name"
100 help="Name of the column containing the quantification values (in the given input file)"/> 105 help="Name of the column containing the quantification values (in the given input file)"/>
106 <param name="multipleMappingSolution" type="select"
107 label="(when using values column above) What to do when multiple items map to the same term"
108 help="When e.g. two Uniprot codes map to the same KEGG code, which quantification value to use">
109 <option value="not" selected="true">Do nothing, leave as is</option>
110 <option value="max" >Use max value</option>
111 <option value="min">Use min value</option>
112 <option value="avg">Use avg value</option>
113 </param>
114 <param name="filterZeros" type="boolean" checked="false"
115 label="Filter zeros"
116 help="Filter out the items that have quantification value = 0"/>
101 </when> 117 </when>
102 <when value="No"> 118 <when value="No">
103 </when> 119 </when>
104 </conditional> 120 </conditional>
105 121
106
107
108
109 122
110 </inputs> 123 </inputs>
111 <outputs> 124 <outputs>
112 #if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__): 125 #if isinstance( $inputFileName.datatype, $__app__.datatypes_registry.get_datatype_by_extension('tabular').__class__):
113 <data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data> 126 <data name="outputFileName" format="tabular" label="${tool.name} on ${on_string}: annotated file " ></data>
114 #else: 127 #else:
115 <data name="outputFileName" format="csv" label="${tool.name} on ${on_string}: annotated file " ></data> 128 <data name="outputFileName" format="csv" label="${tool.name} on ${on_string}: annotated file " ></data>
116 #end if 129 #end if
117 130 #if $genObservations.genObservationsFile == True :
118 <data name="outputObservationsFileName" format="tabular" label="${tool.name} on ${on_string}: term observations file (TSV)"> 131 <data name="outputObservationsFileName" format="tabular" label="${tool.name} on ${on_string}: term observations file (TSV)"></data>
119 <!-- If the expression is false, the file is not created --> 132 #end if
120 <filter>( genObservations.genObservationsFile == True )</filter> 133 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"/>
121 </data>
122 </outputs> 134 </outputs>
123 <tests> 135 <tests>
124 <!-- find out how to use --> 136 <!-- find out how to use -->
125 <test> 137 <test>
126 </test> 138 </test>
185 http://rest.genome.jp/link/compound/hmdb 197 http://rest.genome.jp/link/compound/hmdb
186 198
187 199
188 *Ready to use proteomics links:* 200 *Ready to use proteomics links:*
189 201
190 http://rest.genome.jp/link/uniprot/pti (Phaeodactylum Tri.) 202 http://rest.genome.jp/link/uniprot/pti (Phaeodactylum Tricornutum)
203 http://rest.genome.jp/link/pti/uniprot
191 204
192 http://rest.genome.jp/link/uniprot/hsa (Homo Sapiens) 205 http://rest.genome.jp/link/uniprot/hsa (Homo Sapiens)
193 206
194 (for organism code list see: ) 207 (for organism code list see: )
195 208
196 209
197 Uniprot to GO 210 Uniprot to GO
198 211
199 http://www.uniprot.org/taxonomy/ 212 http://www.uniprot.org/taxonomy/
213
214 http://www.uniprot.org/uniprot/?sort=&amp;desc=&amp;query=proteome:UP000000759&amp;fil=&amp;format=tab&amp;force=yes&amp;columns=id,go-id (Phaeodactylum Tricornutum)
200 215
201 216
202 ----- 217 -----
203 218
204 **Output** 219 **Output**