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annotate xmsannotator_advanced.xml @ 5:47185b5abe9e draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
author recetox
date Mon, 14 Dec 2020 03:33:44 +0000
parents 6b2b2b83b46c
children fff8d90068cd
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1 <tool id="xmsannotator_advanced" name="xMSannotator (advanced)" version="@TOOL_VERSION@+galaxy2">
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2 <macros>
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3 <import>xmsannotator_macros.xml</import>
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4 </macros>
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6 <requirements>
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7 <container type="docker">@DOCKER_IMAGE@</container>
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8 </requirements>
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10 <command detect_errors="aggressive"><![CDATA[
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11 Rscript $wrapper
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12 ]]></command>
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14 <configfiles>
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15 <configfile name="wrapper"><![CDATA[
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16 library(xmsannotator)
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17
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18 annotation <- advanced_annotation(
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19 #if $peak_table.is_of_type("h5")
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20 peak_table = load_peak_table_hdf("${peak_table}"),
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21 #elif $peak_table.is_of_type("parquet")
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22 peak_table = load_peak_table_parquet("${peak_table}"),
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23 #end if
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24 adduct_table = load_adduct_table_parquet("${adduct_table}"),
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25 compound_table = load_compound_table_parquet("${compound_table}"),
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26 mass_tolerance = 1e-6 * ${mass_tolerance_ppm},
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27 time_tolerance = $time_tolerance,
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28 correlation_threshold = as.double($clustering.correlation_threshold),
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29 min_cluster_size = as.integer($clustering.min_cluster_size),
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30 deep_split = as.integer($clustering.deep_split),
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31 network_type = "$clustering.network_type",
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32 #if $scoring.expected_adducts
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33 expected_adducts = load_expected_adducts_csv("${$scoring.expected_adducts_csv}"),
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34 #end if
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35 #if $scoring.boost_compounds
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36 boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds_csv}"),
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37 #end if
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38 redundancy_filtering = $scoring.redundancy_filtering,
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39 n_workers = \${GALAXY_SLOTS:-1}
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40 )
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41
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42 save_parquet(data = annotation, file = "${annotation_parquet}")
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43 ]]></configfile>
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44 </configfiles>
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45
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46 <inputs>
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47 <expand macro="inputs"/>
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48 <expand macro="tolerance">
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49 <param name="time_tolerance" type="float" value="10" min="0">
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50 <label>Retention time tolerance [s]</label>
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51 <help>
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52 Retention time tolerance in seconds for finding peaks derived from the same parent metabolite.
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53 </help>
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54 </param>
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55 </expand>
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56 <section name="clustering" title="Clustering">
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57 <param name="correlation_method" type="select" display="radio" label="Correlation method">
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58 <option value="pearson" selected="true"/>
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59 <option value="spearman"/>
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60 </param>
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61 <param name="correlation_threshold" type="float" value="0.7">
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62 <label>Correlation threshold</label>
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63 <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help>
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64 </param>
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65 <param name="min_cluster_size" type="integer" value="10" min="1">
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66 <label>Minimum cluster size</label>
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67 <help>The minimum number of nodes to be considered as a cluster.</help>
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68 </param>
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69 <param name="deep_split" type="integer" value="2" min="0" max="4">
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70 <label>Deep split</label>
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71 <help>
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72 Deep split provides a rough control over sensitivity to cluster splitting. The higher the value,
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73 the more and smaller clusters will be produced (see WGCNA package documentation).
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74 </help>
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75 </param>
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76 <param name="network_type" type="select" display="radio">
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77 <label>Network type</label>
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78 <help>
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79 Network type parameter affects how the network's adjacency matrix is created from the correlation
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80 matrix (see WGCNA package documentation).
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81 </help>
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82 <option value="signed"/>
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83 <option value="unsigned" selected="true"/>
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84 </param>
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85 </section>
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86 <section name="scoring" title="Scoring" expanded="true">
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87 <param name="strict_boosting" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE">
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88 <label>Strict boosting</label>
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89 <help>
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90 Boost the scores of metabolites that not only belongs to the same pathway but also to the same
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91 cluster. Otherwise, do not account for cluster membership.
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92 </help>
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93 </param>
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94 <param name="expected_adducts" type="data" format="csv,tsv" optional="true">
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95 <label>Expected adducts</label>
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96 <help>
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97 Require the presence of certain adducts for a high confidence match. By default, at least the
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98 presence of an M+H adduct is required for a high confidence match.
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99 </help>
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100 <conversion name="expected_adducts_csv" type="csv"/>
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101 </param>
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102 <param name="boost_compounds" type="data" format="csv,tsv" optional="true">
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103 <label>Validated compounds score boosting (optional)</label>
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104 <help>
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105 Table of previously validated compounds to boost their scores and confidence levels.
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106 The 1st column of the table must contain IDs of compounds.
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107 The optional 2nd and 3rd columns may contain mz values and retention times.
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108 </help>
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109 <conversion name="boost_compounds_csv" type="csv"/>
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110 </param>
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111 <param name="min_isp" type="integer" min="0" value="1">
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112 <label>Minimum number of expected isotopes</label>
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113 <help>
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114 Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
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115 </help>
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116 </param>
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117 <param name="max_isp" type="integer" min="0" value="5">
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118 <label>Maximum number of expected isotopes</label>
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119 <help>
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120 Maximum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
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121 </help>
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122 </param>
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123 <param name="redundancy_filtering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE">
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124 <label>Redundancy filtering</label>
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125 <help>Whether to filter out low-scored multiple matcher or not.</help>
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126 </param>
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127 </section>
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128 </inputs>
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129
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130 <outputs>
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131 <expand macro="outputs"/>
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132 </outputs>
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133
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134 <help><![CDATA[
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135 Annotate the peak intensity table (such as outputted from apLCMS) with compounds from the compounds database
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136 using advanced methods.
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137
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138 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
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139 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are
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140 withing some tolerance. Then, a score and a confidence level is assigned to each match based on peak correlation
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141 clustering, metabolite pathway associations, adducts expectations, and isotope conformations.
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142 ]]></help>
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143
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144 <citations>
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145 <expand macro="citations"/>
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146 </citations>
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147 </tool>