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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
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7 $rankfilter_and_caslookup_combi
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8 $msclust_quant_file
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9 $output_result
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10 "$organism"
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11 "$tissue"
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12 "$experiment_name"
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13 "$user_name"
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14 "$column_type"
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15 </command>
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16 <inputs>
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17 <param format="tabular" name="rankfilter_and_caslookup_combi" type="data" label="RIQC-Combine RankFilter and CasLookup output"
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18 help="Select the (multi) output file from the 'Combine RankFilter and CasLookup' tool"/>
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19 <param format="tabular" name="msclust_quant_file" type="data" label="MusClust-quantification file output"
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20 help="Select the output file from MsClust (centrotype, mic or sim) which also contain respective spectrum details"/>
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21
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22
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23 <param name="organism" type="text" size="80"
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24 label="Organism(s) info"
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25 help="Metadata information to accompany the results when stored in MetExp DB." >
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26 <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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27 </param>
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28
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29 <param name="tissue" type="text" size="80"
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30 label="Tissue(s) info"
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31 help="Metadata information to accompany the results when stored in MetExp DB." >
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32 <validator type="empty_field" message="A value is required."></validator>
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33 </param>
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34
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35 <param name="experiment_name" type="text" size="80"
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36 label="Experiment name/code"
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37 help="Name or code to store the results under. This can help you find the results back in MetExpDB." >
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38 <validator type="empty_field" message="A value is required."></validator>
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39 </param>
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40
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41 <param name="user_name" type="text" size="80"
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42 label="User name"
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43 help="User name or code to store the results under. This can help you find the results back in MetExpDB." >
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44 <validator type="empty_field" message="A value is required."></validator>
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45 </param>
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46
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47 <param name="column_type" type="text" size="80"
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48 label="Column type"
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49 help="Column type to report with the results. This can help you find the results back in MetExpDB." >
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50 <validator type="empty_field" message="A value is required."></validator>
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51 </param>
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52
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53 </inputs>
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54 <outputs>
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55 <data format="tabular" label="${tool.name} on ${on_string}" name="output_result" />
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56 </outputs>
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57 <help>
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58 .. class:: infomark
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59
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60 Tool to combine output from the tools RankFilter, CasLookup and MsClust
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61 into a tabular file that can be uploaded to the METabolomics EXPlorer (MetExp) database.
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62
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63 RankFilter, CasLookup are already combined by 'RIQC-Combine RankFilter and CasLookup' tool so here we will use
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64 this result.
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65
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66 **Notes**
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67
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68 Extra calculations performed:
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69 - 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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70
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71 So in total here we merge 2 files and calculate one new column.
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72
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73
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74 </help>
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75 </tool>
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