Mercurial > repos > tomnl > mspurity_combineannotations

annotate combineAnnotations.xml @ 10:8d5728c85337 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 12:01:27 -0400
parents b1dd803d5164
children 4b7d43c49061
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1 <tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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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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23 --ms1_lookup_resultPth=$ms1_lookup_resultPth
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25 #if $ms1_lookup_checkAdducts:
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26 --ms1_lookup_checkAdducts
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27 #end if
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29 --ms1_lookup_keepAdducts="$ms1_lookup_keepAdducts"
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30 --ms1_lookup_dbSource=$ms1_lookup_dbSource
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31
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32 --sm_weight=$sm_weight
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33 --metfrag_weight=$metfrag_weight
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34 --sirius_csi_weight=$sirius_csi_weight
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35 --probmetab_weight=$probmetab_weight
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36 --ms1_lookup_weight=$ms1_lookup_weight
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37 --biosim_weight=$biosim_weight
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39
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40 #if $create_new_database:
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41 --create_new_database
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42 #end if
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44 --compoundDbType=$compoundDbTypeCond.compoundDbType
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46 #if $compoundDbTypeCond.compoundDbType== 'sqlite'
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47 --compoundDbPth=$compoundDbTypeCond.compoundDbPth
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48 #end if
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49
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51 ]]></command>
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52 <inputs>
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55 <param name="sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
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56 help="The SQLite database generated from msPurity.spectralMatching"/>
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57 <param name="metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true"
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58 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/>
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59 <param name="sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true"
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60 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/>
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61 <param name="probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true"
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62 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID)"/>
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63 <param name="ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular" optional="true"
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64 help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/>
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65 <param name="ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true"
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66 help="Provide a list of adducts that should be used from the MS1 lookup (e.g. [M+H]+, [M+Na]+"/>
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67 <param name="ms1_lookup_checkAdducts" type="boolean" label="MS1 lookup check adducts to CAMERA"
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68 help="Check if adducts match to those found in CAMERA (requires the database to have been created with CAMERA object"/>
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69 <param name="ms1_lookup_dbSource" type="select" label="MS1 lookup database source" help="Which database was used for the MS1 lookup" >
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70 <option value="hmdb" selected="true">hmdb</option>
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71 <option value="pubchem">pubchem</option>
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72 <option value="kegg">kegg</option>
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73 </param>
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74 <param name="sm_weight" type="float" min="0.0" max="1.0" value="0.3" label="Spectral matching weight" help="all weights need to sum to 1" />
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75 <param name="metfrag_weight" type="float" min="0.0" max="1.0" value="0.2" label="Metfrag weight" help="all weights need to sum to 1" />
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76 <param name="sirius_csi_weight" type="float" min="0.0" max="1.0" value="0.2" label="Sirius CSI:FingerID weight" help="all weights need to sum to 1" />
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77 <param name="probmetab_weight" type="float" min="0.0" max="1.0" value="0.0" label="Probmetab weight" help="all weights need to sum to 1" />
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78 <param name="ms1_lookup_weight" type="float" min="0.0" max="1.0" value="0.05" label="MS1 Lookup weight" help="all weights need to sum to 1" />
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79 <param name="biosim_weight" type="float" min="0.0" max="1.0" value="0.25" label="Biological similarity weight" help="all weights need to sum to 1" />
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80 <param name="create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
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81 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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82 When False, the input SQLite database will be updated the results. Use False
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83 if you want to reduce storage space being used."/>
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84
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85 <conditional name="compoundDbTypeCond">
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86 <param name="compoundDbType" type="select" label="compoundDbType" help="Database type for compound database to be used full database available on request - contact t.n.lawson@bham.ac.uk)." >
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87 <option value="sqlite" selected="true">SQLite</option>
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88 <option value="local_config" >Locally configured MySQL, Postgres or SQLite database</option>
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89 </param>
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90 <when value="sqlite">
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91 <param type="data" name="compoundDbPth" label="SQLite compound database pth" format="sqlite" help=""/>
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92 </when>
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93 <when value="local_config">
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94 </when>
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95 <when value="msPurityData">
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96 </when>
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97 </conditional>
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98
0
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99 </inputs>
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100 <outputs>
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101 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
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102 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" />
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103 </outputs>
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104 <tests>
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105 <test>
10
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106 <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" />
0
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107 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
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108 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
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109 <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" />
10
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110 <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" />
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111 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
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112 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />
0
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113 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
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114 </test>
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115 </tests>
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116 <help><![CDATA[
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117 =============================================================
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118 Combine annotation results
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119 =============================================================
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120 -----------
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121 Description
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122 -----------
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123
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124 Tool to combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab
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125 based on weighted scores for each technique aligning each annotation by inchikey and XCMS grouped feature.
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126
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127 See Bioconductor documentation for more details, functions:
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128 msPurity::combineAnnotation()
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129
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130 -----------
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131 Outputs
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132 -----------
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133 * combined_annotation_sqlite
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134 * combined_annotation_tsv
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135
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136 ]]></help>
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137
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138 <expand macro="citations" />
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139
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140 </tool>