# HG changeset patch
# User recetox
# Date 1614084920 0
# Node ID fff8d90068cdff53e1b9bb6ececfb3eddc36c3a7
# Parent  47185b5abe9e1bcc5e7de9a0f816053f6f18acf5
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 8e389d0af707b77bdbf8d55e6fc52e56c0efda33"

diff -r 47185b5abe9e -r fff8d90068cd xmsannotator_advanced.xml
--- a/xmsannotator_advanced.xml	Mon Dec 14 03:33:44 2020 +0000
+++ b/xmsannotator_advanced.xml	Tue Feb 23 12:55:20 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="xmsannotator_advanced" name="xMSannotator (advanced)" version="@TOOL_VERSION@+galaxy2">
+<tool id="xmsannotator_advanced" name="xMSannotator (advanced)" version="@TOOL_VERSION@+galaxy3">
     <macros>
         <import>xmsannotator_macros.xml</import>
     </macros>
@@ -30,10 +30,10 @@
                 deep_split = as.integer($clustering.deep_split),
                 network_type = "$clustering.network_type",
             #if $scoring.expected_adducts
-                expected_adducts = load_expected_adducts_csv("${$scoring.expected_adducts_csv}"),
+                expected_adducts = load_expected_adducts_csv("${scoring.expected_adducts}"),
             #end if
             #if $scoring.boost_compounds
-                boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds_csv}"),
+                boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds}"),
             #end if
                 redundancy_filtering = $scoring.redundancy_filtering,
                 n_workers = \${GALAXY_SLOTS:-1}
@@ -91,22 +91,20 @@
                     cluster. Otherwise, do not account for cluster membership.
                 </help>
             </param>
-            <param name="expected_adducts" type="data" format="csv,tsv" optional="true">
+            <param name="expected_adducts" type="data" format="csv" optional="true">
                 <label>Expected adducts</label>
                 <help>
                     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.
                 </help>
-                <conversion name="expected_adducts_csv" type="csv"/>
             </param>
-            <param name="boost_compounds" type="data" format="csv,tsv" optional="true">
+            <param name="boost_compounds" type="data" format="csv" optional="true">
                 <label>Validated compounds score boosting (optional)</label>
                 <help>
                     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.
                 </help>
-                <conversion name="boost_compounds_csv" type="csv"/>
             </param>
             <param name="min_isp" type="integer" min="0" value="1">
                 <label>Minimum number of expected isotopes</label>