Mercurial > repos > pieterlukasse > prims_metabolomics2
annotate METEXPtools/export_to_metexp_tabular.xml @ 25:9f03c8587d6b draft default tip
MetExp msclust upload format changed from tabular to csv
| author | linda-bakker |
|---|---|
| date | Fri, 24 Aug 2018 09:56:05 -0400 |
| parents | 4393f982d18f |
| children |
| rev | line source |
|---|---|
| 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"/> | |
|
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9f03c8587d6b
MetExp msclust upload format changed from tabular to csv
linda-bakker
parents:
6
diff
changeset
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19 <param format="csv" name="msclust_quant_file" type="data" label="MusClust-quantification file output" |
| 6 | 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> |