Mercurial > repos > recetox > xmsannotator_advanced

comparison xmsannotator_advanced.xml @ 6:fff8d90068cd draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 8e389d0af707b77bdbf8d55e6fc52e56c0efda33"
author recetox
date Tue, 23 Feb 2021 12:55:20 +0000
parents 47185b5abe9e
children 53246490912c
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5:47185b5abe9e 6:fff8d90068cd
1 <tool id="xmsannotator_advanced" name="xMSannotator (advanced)" version="@TOOL_VERSION@+galaxy2"> 1 <tool id="xmsannotator_advanced" name="xMSannotator (advanced)" version="@TOOL_VERSION@+galaxy3">
2 <macros> 2 <macros>
3 <import>xmsannotator_macros.xml</import> 3 <import>xmsannotator_macros.xml</import>
4 </macros> 4 </macros>
5 5
6 <requirements> 6 <requirements>
28 correlation_threshold = as.double($clustering.correlation_threshold), 28 correlation_threshold = as.double($clustering.correlation_threshold),
29 min_cluster_size = as.integer($clustering.min_cluster_size), 29 min_cluster_size = as.integer($clustering.min_cluster_size),
30 deep_split = as.integer($clustering.deep_split), 30 deep_split = as.integer($clustering.deep_split),
31 network_type = "$clustering.network_type", 31 network_type = "$clustering.network_type",
32 #if $scoring.expected_adducts 32 #if $scoring.expected_adducts
33 expected_adducts = load_expected_adducts_csv("${$scoring.expected_adducts_csv}"), 33 expected_adducts = load_expected_adducts_csv("${scoring.expected_adducts}"),
34 #end if 34 #end if
35 #if $scoring.boost_compounds 35 #if $scoring.boost_compounds
36 boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds_csv}"), 36 boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds}"),
37 #end if 37 #end if
38 redundancy_filtering = $scoring.redundancy_filtering, 38 redundancy_filtering = $scoring.redundancy_filtering,
39 n_workers = \${GALAXY_SLOTS:-1} 39 n_workers = \${GALAXY_SLOTS:-1}
40 ) 40 )
41 41
89 <help> 89 <help>
90 Boost the scores of metabolites that not only belongs to the same pathway but also to the same 90 Boost the scores of metabolites that not only belongs to the same pathway but also to the same
91 cluster. Otherwise, do not account for cluster membership. 91 cluster. Otherwise, do not account for cluster membership.
92 </help> 92 </help>
93 </param> 93 </param>
94 <param name="expected_adducts" type="data" format="csv,tsv" optional="true"> 94 <param name="expected_adducts" type="data" format="csv" optional="true">
95 <label>Expected adducts</label> 95 <label>Expected adducts</label>
96 <help> 96 <help>
97 Require the presence of certain adducts for a high confidence match. By default, at least the 97 Require the presence of certain adducts for a high confidence match. By default, at least the
98 presence of an M+H adduct is required for a high confidence match. 98 presence of an M+H adduct is required for a high confidence match.
99 </help> 99 </help>
100 <conversion name="expected_adducts_csv" type="csv"/>
101 </param> 100 </param>
102 <param name="boost_compounds" type="data" format="csv,tsv" optional="true"> 101 <param name="boost_compounds" type="data" format="csv" optional="true">
103 <label>Validated compounds score boosting (optional)</label> 102 <label>Validated compounds score boosting (optional)</label>
104 <help> 103 <help>
105 Table of previously validated compounds to boost their scores and confidence levels. 104 Table of previously validated compounds to boost their scores and confidence levels.
106 The 1st column of the table must contain IDs of compounds. 105 The 1st column of the table must contain IDs of compounds.
107 The optional 2nd and 3rd columns may contain mz values and retention times. 106 The optional 2nd and 3rd columns may contain mz values and retention times.
108 </help> 107 </help>
109 <conversion name="boost_compounds_csv" type="csv"/>
110 </param> 108 </param>
111 <param name="min_isp" type="integer" min="0" value="1"> 109 <param name="min_isp" type="integer" min="0" value="1">
112 <label>Minimum number of expected isotopes</label> 110 <label>Minimum number of expected isotopes</label>
113 <help> 111 <help>
114 Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match. 112 Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match.