6
+ − 1 <tool id="export_to_metexp_tabular"
+ − 2 name="METEXP - Tabular file"
+ − 3 version="0.2.0">
+ − 4 <description>Create tabular file for loading into METabolomics EXPlorer database</description>
+ − 5 <command interpreter="python">
+ − 6 export_to_metexp_tabular.py
+ − 7 $rankfilter_and_caslookup_combi
+ − 8 $msclust_quant_file
+ − 9 $output_result
+ − 10 "$organism"
+ − 11 "$tissue"
+ − 12 "$experiment_name"
+ − 13 "$user_name"
+ − 14 "$column_type"
+ − 15 </command>
+ − 16 <inputs>
+ − 17 <param format="tabular" name="rankfilter_and_caslookup_combi" type="data" label="RIQC-Combine RankFilter and CasLookup output"
+ − 18 help="Select the (multi) output file from the 'Combine RankFilter and CasLookup' tool"/>
+ − 19 <param format="tabular" name="msclust_quant_file" type="data" label="MusClust-quantification file output"
+ − 20 help="Select the output file from MsClust (centrotype, mic or sim) which also contain respective spectrum details"/>
+ − 21
+ − 22
+ − 23 <param name="organism" type="text" size="80"
+ − 24 label="Organism(s) info"
+ − 25 help="Metadata information to accompany the results when stored in MetExp DB." >
+ − 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 -->
+ − 27 </param>
+ − 28
+ − 29 <param name="tissue" type="text" size="80"
+ − 30 label="Tissue(s) info"
+ − 31 help="Metadata information to accompany the results when stored in MetExp DB." >
+ − 32 <validator type="empty_field" message="A value is required."></validator>
+ − 33 </param>
+ − 34
+ − 35 <param name="experiment_name" type="text" size="80"
+ − 36 label="Experiment name/code"
+ − 37 help="Name or code to store the results under. This can help you find the results back in MetExpDB." >
+ − 38 <validator type="empty_field" message="A value is required."></validator>
+ − 39 </param>
+ − 40
+ − 41 <param name="user_name" type="text" size="80"
+ − 42 label="User name"
+ − 43 help="User name or code to store the results under. This can help you find the results back in MetExpDB." >
+ − 44 <validator type="empty_field" message="A value is required."></validator>
+ − 45 </param>
+ − 46
+ − 47 <param name="column_type" type="text" size="80"
+ − 48 label="Column type"
+ − 49 help="Column type to report with the results. This can help you find the results back in MetExpDB." >
+ − 50 <validator type="empty_field" message="A value is required."></validator>
+ − 51 </param>
+ − 52
+ − 53 </inputs>
+ − 54 <outputs>
+ − 55 <data format="tabular" label="${tool.name} on ${on_string}" name="output_result" />
+ − 56 </outputs>
+ − 57 <help>
+ − 58 .. class:: infomark
+ − 59
+ − 60 Tool to combine output from the tools RankFilter, CasLookup and MsClust
+ − 61 into a tabular file that can be uploaded to the METabolomics EXPlorer (MetExp) database.
+ − 62
+ − 63 RankFilter, CasLookup are already combined by 'RIQC-Combine RankFilter and CasLookup' tool so here we will use
+ − 64 this result.
+ − 65
+ − 66 **Notes**
+ − 67
+ − 68 Extra calculations performed:
+ − 69 - The columns MM and MW are also added here and are derived from the column FORMULA found in RankFilter, CasLookup combined result.
+ − 70
+ − 71 So in total here we merge 2 files and calculate one new column.
+ − 72
+ − 73
+ − 74 </help>
+ − 75 </tool>
