Mercurial > repos > recetox > october_recetox_xmsannotator_advanced

annotate october_recetox_xmsannotator_advanced.xml @ 13:29b04e82bc4e draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 42e346be32aa2c3f33fb2693bfc3675b1cf57397"
author recetox
date Wed, 03 Nov 2021 12:35:35 +0000
parents c1f439401578
children 51f8e69c9d47
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1 <tool id="october_recetox_xmsannotator_advanced" name="OCTOBER RECETOX xMSannotator advanced" version="@TOOL_VERSION@+galaxy3">
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2 <description>annotate peak intensity table including scores and confidence levels</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="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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12 <configfiles>
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13 <configfile name="wrapper"><![CDATA[
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14 library(recetox.xmsannotator)
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16 annotation <- advanced_annotation(
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17 #if $peak_table.is_of_type("parquet")
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18 peak_table = load_peak_table_parquet("${peak_table}"),
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19 #end if
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20 adduct_table = load_adduct_table_parquet("${adduct_table}"),
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21 adduct_weights = as.data.frame(read.csv("${adduct_weights}")),
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22 compound_table = load_compound_table_parquet("${compound_table}"),
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23 mass_tolerance = 1e-6 * ${mass_tolerance_ppm},
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24 time_tolerance = $time_tolerance,
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25 correlation_threshold = as.double($clustering.correlation_threshold),
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26 min_cluster_size = as.integer($clustering.min_cluster_size),
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27 deep_split = as.integer($clustering.deep_split),
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28 network_type = "$clustering.network_type",
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29 redundancy_filtering = $scoring.redundancy_filtering,
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30 n_workers = n_workers,
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31 intensity_deviation_tolerance = as.double($intensity_deviation_tolerance),
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32 mass_defect_tolerance = as.double($mass_defect_tolerance),
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33 mass_defect_precision = as.double($mass_defect_precision),
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34 peak_rt_width = as.integer($peak_rt_width),
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35 maximum_isotopes = as.integer($maximum_isotopes),
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36 min_ions_per_chemical = as.integer($min_ions_per_chemical),
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37 filter_by = $filter_by
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38 )
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39 save_parquet(data = annotation, file = "${annotation_parquet}")
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40 ]]></configfile>
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41 </configfiles>
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42
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43 <inputs>
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44 <expand macro="inputs"/>
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45 <expand macro="tolerance">
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46 <param name="time_tolerance" type="float" value="10" min="0">
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47 <label>Retention time tolerance [s]</label>
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48 <help>
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49 Retention time tolerance in seconds for finding peaks derived from the same parent compound.
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50 </help>
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51 </param>
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52 </expand>
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53 <section name="clustering" title="Clustering">
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54 <param name="correlation_threshold" type="float" value="0.7">
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55 <label>Correlation threshold</label>
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56 <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help>
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57 </param>
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58 <param name="min_cluster_size" type="integer" value="10" min="1">
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59 <label>Minimum cluster size</label>
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60 <help>The minimum number of nodes to be considered as a cluster.</help>
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61 </param>
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62 <param name="deep_split" type="integer" value="2" min="0" max="4">
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63 <label>Deep split</label>
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64 <help>
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65 Deep split provides a rough control over sensitivity to cluster splitting. The higher the value,
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66 the more and smaller clusters will be produced (see WGCNA package documentation).
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67 </help>
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68 </param>
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69 <param name="network_type" type="select" display="radio">
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70 <label>Network type</label>
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71 <help>
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72 Network type parameter affects how the network's adjacency matrix is created from the correlation
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73 matrix (see WGCNA package documentation).
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74 </help>
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75 <option value="signed">Signed</option>
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76 <option value="unsigned" selected="true">Unsigned</option>
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77 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
78 </section>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
79 <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:
diff changeset
80 <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:
diff changeset
81 <label>Strict boosting</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
82 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
83 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
84 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
85 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
86 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
87 <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
parents:
diff changeset
88 <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
parents:
diff changeset
89 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
90 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
parents:
diff changeset
91 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
92 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
93 <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
parents:
diff changeset
94 <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
parents:
diff changeset
95 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
96 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:
diff changeset
97 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
98 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
99 <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:
diff changeset
100 <label>Redundancy filtering</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
101 <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
parents:
diff changeset
102 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
103 </section>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
104 <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:
diff changeset
105 <label>intensity_deviation_tolerance</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
106 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
107 <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
108 <label>mass_defect_tolerance</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
109 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
110 <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
111 <label>mass_defect_precision</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
112 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
113 <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
parents:
diff changeset
114 <label>peak_rt_width</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
115 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
116 <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
parents:
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117 <label>maximum_isotopes</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
118 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
119 <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
parents:
diff changeset
120 <label>min_ions_per_chemical</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
121 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
122 <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
123 <!-- 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
124 <sanitizer sanitize="false"></sanitizer>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
125 <label>filter_by</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
126 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
127 </inputs>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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128
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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129 <outputs>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
130 <expand macro="outputs"/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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131 </outputs>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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132
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
133 <help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
134 <![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
135 @HELP@
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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diff changeset
136 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"
recetox
parents:
diff changeset
137 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"
recetox
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138 ]]>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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139 </help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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140
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
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141 <citations>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
parents:
diff changeset
142 <expand macro="citations"/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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143 </citations>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
recetox
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144 </tool>