# HG changeset patch
# User recetox
# Date 1628766779 0
# Node ID 7807fbeb1388823cd684af9180ace584da5fbf3f
# Parent 1c70b19b09ebe302819ed99102d2d245ab6ce2a9
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
diff -r 1c70b19b09eb -r 7807fbeb1388 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Aug 12 11:12:59 2021 +0000
@@ -0,0 +1,57 @@
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+ 0.9.0
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+ r-recetox-xmsannotator
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+ mz and rt.
+ ]]>
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+ compound_id, monoisotopic_mass, and molecular_formula.
+ ]]>
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+ adduct, charge, mass, and n_molecules.
+ ]]>
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+ Mass tolerance in ppm for database matching.
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+ 10.1021/acs.analchem.6b01214
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diff -r 1c70b19b09eb -r 7807fbeb1388 recetox_xmsannotator_advanced.xml
--- a/recetox_xmsannotator_advanced.xml Thu Sep 17 08:40:19 2020 +0000
+++ b/recetox_xmsannotator_advanced.xml Thu Aug 12 11:12:59 2021 +0000
@@ -1,73 +1,141 @@
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- recetox_xmsannotator_macros.xml
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\ No newline at end of file
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+ annotate peak intensity table including scores and confidence levels
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+ macros.xml
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+ Retention time tolerance in seconds for finding peaks derived from the same parent metabolite.
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+ Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.
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+ The minimum number of nodes to be considered as a cluster.
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+ Deep split provides a rough control over sensitivity to cluster splitting. The higher the value,
+ the more and smaller clusters will be produced (see WGCNA package documentation).
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+ Network type parameter affects how the network's adjacency matrix is created from the correlation
+ matrix (see WGCNA package documentation).
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+ Boost the scores of metabolites that not only belongs to the same pathway but also to the same
+ cluster. Otherwise, do not account for cluster membership.
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+ Require the presence of certain adducts for a high confidence match. By default, at least the
+ presence of an M+H adduct is required for a high confidence match.
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+ Table of previously validated compounds to boost their scores and confidence levels.
+ The 1st column of the table must contain IDs of compounds.
+ The optional 2nd and 3rd columns may contain mz values and retention times.
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+ Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
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+ Maximum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
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+ Whether to filter out low-scored multiple matcher or not.
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diff -r 1c70b19b09eb -r 7807fbeb1388 recetox_xmsannotator_macros.xml
--- a/recetox_xmsannotator_macros.xml Thu Sep 17 08:40:19 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
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- recetox_datatypes
- registry.gitlab.ics.muni.cz:443/recetox/mass-spectrometry/xmsannotator:v2.0
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- 10.1021/acs.analchem.6b01214
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\ No newline at end of file
diff -r 1c70b19b09eb -r 7807fbeb1388 tool-data/recetox_metabolite_databases.loc.sample
--- a/tool-data/recetox_metabolite_databases.loc.sample Thu Sep 17 08:40:19 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-# This file has the format (white space characters are
-# TAB characters):
-#
-#
-#
\ No newline at end of file
diff -r 1c70b19b09eb -r 7807fbeb1388 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Thu Sep 17 08:40:19 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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