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annotate export_to_metexp_tabular.xml @ 26:637830ac8bcd

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added validation in metexp to tabular tool; added workaround/fix for L and D compound types
author pieter.lukasse@wur.nl
date Thu, 24 Apr 2014 11:28:38 +0200
parents 19d8fd10248e
children ecd3f6c9e606
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1 <tool id="export_to_metexp_tabular"
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2 name="METEXP - Tabular file"
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3 version="0.2.0">
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4 <description>Create tabular file for loading into METabolomics EXPlorer database</description>
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5 <command interpreter="python">
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6 export_to_metexp_tabular.py $rankfilter_and_caslookup_combi $msclust_quant_file $output_result
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7 $organism $tissue $experiment_name $user_name $column_type
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8 </command>
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9 <inputs>
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10 <param format="tabular" name="rankfilter_and_caslookup_combi" type="data" label="RIQC-Combine RankFilter and CasLookup output"
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11 help="Select the (multi) output file from the 'Combine RankFilter and CasLookup' tool"/>
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12 <param format="tabular" name="msclust_quant_file" type="data" label="MusClust-quantification file output"
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13 help="Select the output file from MsClust (centrotype, mic or sim) which also contain respective spectrum details"/>
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16 <param name="organism" type="text" size="80"
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17 label="Organism(s) info"
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18 help="Metadata information to accompany the results when stored in MetExp DB." >
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19 <validator type="empty_field" message="A value is required."></validator><!-- attribute optional="False" does not seem to work for params so validator is added -->
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20 </param>
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21
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22 <param name="tissue" type="text" size="80"
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23 label="Tissue(s) info"
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24 help="Metadata information to accompany the results when stored in MetExp DB." >
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25 <validator type="empty_field" message="A value is required."></validator>
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26 </param>
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28 <param name="experiment_name" type="text" size="80"
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29 label="Experiment name/code"
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30 help="Name or code to store the results under. This can help you find the results back in MetExpDB." >
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31 <validator type="empty_field" message="A value is required."></validator>
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32 </param>
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34 <param name="user_name" type="text" size="80"
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35 label="User name"
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36 help="User name or code to store the results under. This can help you find the results back in MetExpDB." >
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37 <validator type="empty_field" message="A value is required."></validator>
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38 </param>
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40 <param name="column_type" type="text" size="80"
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41 label="Column type"
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42 help="Column type to report with the results. This can help you find the results back in MetExpDB." >
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43 <validator type="empty_field" message="A value is required."></validator>
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44 </param>
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46 </inputs>
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47 <outputs>
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48 <data format="tabular" label="${tool.name} on ${on_string}" name="output_result" />
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49 </outputs>
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50 <help>
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51 .. class:: infomark
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52
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53 Tool to combine output from the tools RankFilter, CasLookup and MsClust
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54 into a tabular file that can be uploaded to the METabolomics EXPlorer (MetExp) database.
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56 RankFilter, CasLookup are already combined by 'RIQC-Combine RankFilter and CasLookup' tool so here we will use
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57 this result.
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58
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59 **Notes**
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60
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61 Extra calculations performed:
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62 - The columns MM and MW are also added here and are derived from the column FORMULA found in RankFilter, CasLookup combined result.
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64 So in total here we merge 2 files and calculate one new column.
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67 </help>
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68 </tool>