Mercurial > repos > tomnl > mspurity_combineannotations

annotate combineAnnotations.xml @ 1:75507d2e856c draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e67cf7a95ce430d1d373c03992a615da2f3eeeb1
author tomnl
date Tue, 04 Jun 2019 10:52:35 -0400
parents d6350a637d4a
children b22aa0a9fc25
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75507d2e856c planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e67cf7a95ce430d1d373c03992a615da2f3eeeb1
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1 <tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="0.2.1">
0
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2 <description>
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3 Combine, score and rank metabolite annotation results
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4 </description>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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10 <expand macro="requirements">
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11 </expand>
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13 <stdio>
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14 <exit_code range="1:" />
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15 </stdio>
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16 <command interpreter="Rscript"><![CDATA[
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17 combineAnnotations.R
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18 --sm_resultPth="$sm_resultPth"
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19 --metfrag_resultPth="$metfrag_resultPth"
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20 --sirius_csi_resultPth="$sirius_csi_resultPth"
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21 --probmetab_resultPth="$probmetab_resultPth"
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22 --sm_weight=$sm_weight
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23 --metfrag_weight=$metfrag_weight
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24 --sirius_csi_weight=$sirius_csi_weight
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25 --probmetab_weight=$probmetab_weight
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26 #if $create_new_database:
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27 --create_new_database
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28 #end if
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29
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30 ]]></command>
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31 <inputs>
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32 <param name="sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
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33 help="The SQLite database generated from msPurity.spectralMatching"/>
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34 <param name="metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular"
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35 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
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36 <param name="sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular"
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37 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
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38 <param name="probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular"
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39 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
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40 <param name="sm_weight" type="float" min="0.0" max="1.0" value="0.4" label="Spectral matching weight" help="all weights need to sum to 1" />
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41 <param name="metfrag_weight" type="float" min="0.0" max="1.0" value="0.25" label="Metfrag weight" help="all weights need to sum to 1" />
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42 <param name="sirius_csi_weight" type="float" min="0.0" max="1.0" value="0.25" label="Sirius CSI:FingerID weight" help="all weights need to sum to 1" />
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43 <param name="probmetab_weight" type="float" min="0.0" max="1.0" value="0.1" label="Probmetab weight" help="all weights need to sum to 1" />
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44 <param name="create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
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45 help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy.
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46 When False, the input SQLite database will be updated the results. Use False
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47 if you want to reduce storage space being used."/>
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48 </inputs>
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49 <outputs>
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50 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
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51 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="sm_resultPth" value="spectralMatching_db_with_spectral_matching.sqlite" />
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56 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
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57 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
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58 <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" />
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59 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" >
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60 <assert_contents>
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61 <has_n_columns n="32" />
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62 </assert_contents>
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63 </output>
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64 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 =============================================================
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69 Combine annotation results
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70 =============================================================
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71 -----------
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72 Description
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73 -----------
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74
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75 Tool to combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab
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76 based on weighted scores for each technique aligning each annotation by inchikey and XCMS grouped feature.
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77
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78 See Bioconductor documentation for more details, functions:
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79 msPurity::combineAnnotation()
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80
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81 -----------
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82 Outputs
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83 -----------
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84 * combined_annotation_sqlite
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85 * combined_annotation_tsv
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86
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87 ]]></help>
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88
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89 <expand macro="citations" />
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90
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91 </tool>