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1 <tool id="query_metexp"
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2 name="METEXP - Query Database "
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3 version="0.1.0">
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4 <description>Query a set of identifications against the METabolomics EXPeriments database</description>
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5 <command interpreter="python">
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6 query_metexp.py
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7 $input_file
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8 "$casid_col"
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9 "$formula_col"
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10 "$molecular_mass_col"
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11 "$metexp_dblink_file"
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12 $separation_method
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13 $output_result
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14 </command>
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15 <inputs>
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16
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17 <param name="input_file" format="tabular" type="data"
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18 label="Input file"
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19 help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/>
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20
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21 <param name="separation_method" type="select" label="Data type to query">
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22 <option value="GC" selected="True">GC</option>
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23 <option value="LC">LC</option>
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24 </param>
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25
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26
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27 <param name="casid_col" type="text" size="50"
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28 label="CAS ID column name"
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29 value="CAS"
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30 help="Name of the column containing the CAS code information (in the given input file)" />
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31 <param name="formula_col" type="text" size="50"
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32 label="Formula ID column name"
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33 value="FORMULA"
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34 help="Name of the column containing the formula information (in the given input file)" />
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35 <param name="molecular_mass_col" type="text" size="50"
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36 label="Molecular mass column name"
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37 value="MM"
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38 help="Name of the column containing the molecular mass information (in the given input file)" />
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39
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40 <param name="metexp_dblink_file" type="select" label="MetExp DB to query"
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41 help="Select the MetExp Database/backend which should be queried"
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42 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_Databases")'/>
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43
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44
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45 </inputs>
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46 <outputs>
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47 <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" />
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48 </outputs>
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49 <code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
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50 <help>
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51 .. class:: infomark
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52
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53 This tool will Query a set of identifications against the METabolomics EXPlorer database.
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54
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55 It will take the input file and for each record it will query the
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56 molecular mass in the selected MetExp DB. If one or more compounds are found in the
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57 MetExp DB then extra information regarding these compounds is added to the output file.
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58
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59 The output file is thus the input file enriched with information about
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60 related items found in the selected MetExp DB.
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61
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62 **Notes**
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63
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64 The input file can be any tabular file, as long as it contains a column for the molecular mass
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65 and one for the formula of the respective identification.
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66
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67
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68 </help>
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69 </tool>
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