annotate combineAnnotations.xml @ 6:18c0038dde9c draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:33:09 +0000
parents d4376a743f7b
children 94a2b6571758
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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>Combine, score and rank metabolite annotation results</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$__tool_directory__/combineAnnotations.R'
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9 --sm_resultPth='$sm_resultPth'
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10 --metfrag_resultPth='$metfrag_resultPth'
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11 --sirius_csi_resultPth='$sirius_csi_resultPth'
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13 #if $probmetabCond.probmetabChoice == 'probmetab'
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14 --probmetab_resultPth='$probmetabCond.probmetab_resultPth'
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15 #end if
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17 --ms1_lookup_resultPth='$ms1_lookup_resultPth'
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19 #if $ms1_lookup_checkAdducts:
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20 --ms1_lookup_checkAdducts
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21 #end if
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23 --ms1_lookup_keepAdducts='$ms1_lookup_keepAdducts'
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24 --ms1_lookup_dbSource=$ms1_lookup_dbSource
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26 --sm_weight=$sm_weight
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27 --metfrag_weight=$metfrag_weight
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28 --sirius_csi_weight=$sirius_csi_weight
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29 --probmetab_weight=$probmetab_weight
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30 --ms1_lookup_weight=$ms1_lookup_weight
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31 --biosim_weight=$biosim_weight
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34 #if $create_new_database:
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35 --create_new_database
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36 #end if
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38 --compoundDbType=$compoundDbTypeCond.compoundDbType
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39
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40 #if $compoundDbTypeCond.compoundDbType== 'sqlite'
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41 --compoundDbPth='$compoundDbTypeCond.compoundDbPth'
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42 #end if
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43
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44 #if $summaryOutput:
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45 --summaryOutput
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46 #end if
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47
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49 ]]></command>
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50 <inputs>
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51
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52
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53 <param argument="--sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
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54 help="The SQLite database generated from msPurity.spectralMatching"/>
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55 <param argument="--metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true"
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56 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/>
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57 <param argument="--sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true"
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58 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/>
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59 <conditional name="probmetabCond">
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60 <param name="probmetabChoice" type="select" label="Use probmetab data" help="The result of the Probmetab analysis" >
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61 <option value="no_probmetab" selected="true" >Do not include probmetab results</option>
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62 <option value="probmetab" >Include probmetab results</option>
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63 </param>
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64 <when value="probmetab">
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65 <param argument="--probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true"
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66 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID). Alternatively any ms1 annotation tool can be used
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67 instead of probmetab"/>
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68 </when>
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69 <when value="no_probmetab">
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70 </when>
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71 </conditional>
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72 <param argument="--ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular" optional="true"
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73 help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/>
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74 <param argument="--ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true"
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75 help="Provide a list of adducts that should be used from the MS1 lookup (e.g. [M+H]+, [M+Na]+"/>
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76 <param argument="--ms1_lookup_checkAdducts" type="boolean" label="MS1 lookup check adducts to CAMERA"
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77 help="Check if adducts match to those found in CAMERA (requires the database to have been created with CAMERA object"/>
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78 <param argument="--ms1_lookup_dbSource" type="select" label="MS1 lookup database source" help="Which database was used for the MS1 lookup" >
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79 <option value="hmdb" selected="true">hmdb</option>
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80 <option value="pubchem">pubchem</option>
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81 <option value="kegg">kegg</option>
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82 </param>
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83 <param argument="--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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84 <param argument="--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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85 <param argument="--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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86 <param argument="--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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87 <param argument="--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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88 <param argument="--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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89 <param argument="--summaryOutput" type="boolean" checked="true" label="Create summary output" help="Create tab separated file of all annotations and features"/>
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90 <param argument="--create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
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91 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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92 When False, the input SQLite database will be updated the results. Use False
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93 if you want to reduce storage space being used."/>
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94
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95 <conditional name="compoundDbTypeCond">
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96 <param argument="--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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97 <option value="sqlite" selected="true">SQLite</option>
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98 <option value="local_config" >Locally configured MySQL, Postgres or SQLite database</option>
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99 </param>
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100 <when value="sqlite">
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101 <param argument="--compoundDbPth" type="data" label="SQLite compound database pth" format="sqlite" help=""/>
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102 </when>
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103 <when value="local_config">
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104 </when>
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105 </conditional>
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106
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107 </inputs>
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108 <outputs>
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109 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
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110 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" />
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111 </outputs>
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112 <tests>
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113 <test>
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114 <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" />
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115 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
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116 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
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117 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
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118 <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" />
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119 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
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120 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />
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121 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
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122 </test>
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123 </tests>
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124 <help><![CDATA[
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125 =============================================================
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126 Combine annotation results
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127 =============================================================
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128 -----------
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129 Description
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130 -----------
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131
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132 Tool to combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab
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133 based on weighted scores for each technique aligning each annotation by inchikey and XCMS grouped feature.
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134
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135 See Bioconductor documentation for more details, functions:
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136 msPurity::combineAnnotation()
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137
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138 -----------
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139 Outputs
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140 -----------
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141 * combined_annotation_sqlite
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142 * combined_annotation_tsv
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143
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144 ]]></help>
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145
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146 <expand macro="citations" />
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147
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148 </tool>