Mercurial > repos > tomnl > mspurity_combineannotations

annotate combineAnnotations.xml @ 3:b22aa0a9fc25 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty
author tomnl
date Tue, 18 Jun 2019 10:08:40 -0400
parents 75507d2e856c
children 68c405751ef6
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1 <tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="0.2.2">
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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 #if $eic
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30 --eic
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31 #end if
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32
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33 ]]></command>
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34 <inputs>
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35 <param name="sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
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36 help="The SQLite database generated from msPurity.spectralMatching"/>
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37 <param name="metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true"
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38 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
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39 <param name="sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true"
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40 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
3
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41 <param name="probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true"
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42 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
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43 <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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44 <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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45 <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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46 <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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47 <param name="create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
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48 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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49 When False, the input SQLite database will be updated the results. Use False
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50 if you want to reduce storage space being used."/>
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51 <param name="eic" type="boolean" label="Include EIC data?"
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52 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
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53 the database. Note, this will take considerable time for large datasets and
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54 the resulting SQLite database can be large"/>
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55 </inputs>
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56 <outputs>
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57 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
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58 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" />
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="sm_resultPth" value="spectralMatching_db_with_spectral_matching.sqlite" />
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63 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
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64 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
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65 <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" />
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66 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" >
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67 <assert_contents>
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68 <has_n_columns n="32" />
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69 </assert_contents>
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70 </output>
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71 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 =============================================================
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76 Combine annotation results
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77 =============================================================
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78 -----------
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79 Description
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80 -----------
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81
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82 Tool to combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab
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83 based on weighted scores for each technique aligning each annotation by inchikey and XCMS grouped feature.
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84
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85 See Bioconductor documentation for more details, functions:
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86 msPurity::combineAnnotation()
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87
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88 -----------
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89 Outputs
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90 -----------
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91 * combined_annotation_sqlite
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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92 * combined_annotation_tsv
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94 ]]></help>
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96 <expand macro="citations" />
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97
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98 </tool>