Mercurial > repos > recetox > october_recetox_xmsannotator_advanced

annotate october_recetox_xmsannotator_advanced.xml @ 0:e2e2e455fcfb draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
author recetox
date Fri, 29 Oct 2021 09:49:13 +0000
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children 8fcf5ca25f5d
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e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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1 <tool id="october_recetox_xmsannotator_advanced" name="OCTOBER RECETOX xMSannotator advanced" version="@TOOL_VERSION@+galaxy0">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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2 <description>annotate peak intensity table including scores and confidence levels</description>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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3 <macros>
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4 <import>macros.xml</import>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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5 </macros>
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6 <expand macro="creator"/>
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7 <expand macro="requirements" />
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8 <command detect_errors="aggressive"><![CDATA[
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9 Rscript -e "n_workers <- \${GALAXY_SLOTS:-1}" -e "source('${wrapper}')"
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10 ]]></command>
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11
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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12 <configfiles>
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13 <configfile name="wrapper"><![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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14 library(recetox.xmsannotator)
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15
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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16 annotation <- advanced_annotation(
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17 #if $peak_table.is_of_type("parquet")
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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18 peak_table = load_peak_table_parquet("${peak_table}"),
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19 #end if
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20 adduct_table = load_adduct_table_parquet("${adduct_table}"),
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21 compound_table = load_compound_table_parquet("${compound_table}"),
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22 mass_tolerance = 1e-6 * ${mass_tolerance_ppm},
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23 time_tolerance = $time_tolerance,
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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24 correlation_threshold = as.double($clustering.correlation_threshold),
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25 min_cluster_size = as.integer($clustering.min_cluster_size),
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26 deep_split = as.integer($clustering.deep_split),
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27 network_type = "$clustering.network_type",
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28 ## #if $scoring.expected_adducts
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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29 ## expected_adducts = load_expected_adducts_csv("${scoring.expected_adducts}"),
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30 ## #end if
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31 ## #if $scoring.boost_compounds
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32 ## boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds}"),
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33 ## #end if
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34 redundancy_filtering = $scoring.redundancy_filtering,
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35 n_workers = n_workers,
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36 ## new params
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37 intensity_deviation_tolerance = as.double($intensity_deviation_tolerance),
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38 mass_defect_tolerance = as.double($mass_defect_tolerance),
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39 mass_defect_precision = as.double($mass_defect_precision),
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40 peak_rt_width = as.integer($peak_rt_width),
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41 maximum_isotopes = as.integer($maximum_isotopes),
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42 min_ions_per_chemical = as.integer($min_ions_per_chemical),
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43 filter_by = "$filter_by"
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44 )
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45
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46 save_parquet(data = annotation, file = "${annotation_parquet}")
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47 ]]></configfile>
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48 </configfiles>
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49
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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50 <inputs>
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51 <expand macro="inputs"/>
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52 <expand macro="tolerance">
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53 <param name="time_tolerance" type="float" value="10" min="0">
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54 <label>Retention time tolerance [s]</label>
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55 <help>
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56 Retention time tolerance in seconds for finding peaks derived from the same parent compound.
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57
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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58 </help>
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59 </param>
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60 </expand>
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61 <section name="clustering" title="Clustering">
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62 <param name="correlation_method" type="select" display="radio" label="Correlation method">
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63 <option value="pearson" selected="true"/>
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64 <option value="spearman"/>
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65 </param>
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66 <param name="correlation_threshold" type="float" value="0.7">
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67 <label>Correlation threshold</label>
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68 <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help>
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69 </param>
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70 <param name="min_cluster_size" type="integer" value="10" min="1">
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71 <label>Minimum cluster size</label>
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72 <help>The minimum number of nodes to be considered as a cluster.</help>
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73 </param>
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74 <param name="deep_split" type="integer" value="2" min="0" max="4">
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75 <label>Deep split</label>
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76 <help>
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77 Deep split provides a rough control over sensitivity to cluster splitting. The higher the value,
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diff changeset
78 the more and smaller clusters will be produced (see WGCNA package documentation).
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
79 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
80 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
81 <param name="network_type" type="select" display="radio">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
82 <label>Network type</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
83 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
84 Network type parameter affects how the network's adjacency matrix is created from the correlation
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
85 matrix (see WGCNA package documentation).
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
86 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
87 <option value="signed"/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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88 <option value="unsigned" selected="true"/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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89 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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90 </section>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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91 <section name="scoring" title="Scoring" expanded="true">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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92 <param name="strict_boosting" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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93 <label>Strict boosting</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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94 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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95 Boost the scores of metabolites that not only belongs to the same pathway but also to the same
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
96 cluster. Otherwise, do not account for cluster membership.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
97 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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98 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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99 <!-- <param name="expected_adducts" type="data" format="csv" optional="true">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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100 <label>Expected adducts (optional)</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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101
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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102 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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103 Require the presence of certain adducts for a high confidence match. By default, at least the
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
104 presence of an M+H adduct is required for a high confidence match.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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105 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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106 </param> -->
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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107 <!-- <param name="boost_compounds" type="data" format="csv" optional="true">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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108 <label>Validated compounds score boosting (optional)</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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109 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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110 Table of previously validated compounds to boost their scores and confidence levels.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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111 The 1st column of the table must contain IDs of compounds.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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112 The optional 2nd and 3rd columns may contain mz values and retention times.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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113 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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114 </param> -->
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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115 <param name="min_isp" type="integer" min="0" value="1">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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116 <label>Minimum number of expected isotopes</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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117 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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118 Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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119 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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120 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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121 <param name="max_isp" type="integer" min="0" value="5">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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122 <label>Maximum number of expected isotopes</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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123 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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124 Maximum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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125 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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126 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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127 <param name="redundancy_filtering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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128 <label>Redundancy filtering</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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129 <help>Whether to filter out low-scored multiple matcher or not.</help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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130 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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131 </section>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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132 <param name="intensity_deviation_tolerance" type="float" value="0.1">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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133 <label>intensity_deviation_tolerance</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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134 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
135 <param name="mass_defect_tolerance" type="float" value="0.1">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
136 <label>mass_defect_tolerance</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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137 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
138 <param name="mass_defect_precision" type="float" value="0.01">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
139 <label>mass_defect_precision</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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140 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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diff changeset
141 <param name="peak_rt_width" type="integer" value="1">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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142 <label>peak_rt_width</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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143 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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144 <param name="maximum_isotopes" type="integer" value="10">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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145 <label>maximum_isotopes</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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146 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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147 <param name="min_ions_per_chemical" type="integer" value="2">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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148 <label>min_ions_per_chemical</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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149 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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150 <param name="filter_by" type="text" value="c('M-H', 'M+H')">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
151 <!-- turn sanitizer off for prototype, TODO refactor this for production -->
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
152 <sanitizer sanitize="false"></sanitizer>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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153 <label>filter_by</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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154 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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155 </inputs>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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156
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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157 <outputs>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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158 <expand macro="outputs"/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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159 </outputs>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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160
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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161 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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162 <![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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163 @HELP@
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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164 Then, a score and a confidence level is assigned to each match based on peak correlation
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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165 clustering, metabolite pathway associations, adducts expectations, and isotope conformations.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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166 ]]>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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167 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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168
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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169 <citations>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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170 <expand macro="citations"/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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171 </citations>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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172 </tool>