Mercurial > repos > recetox > xmsannotator_advanced

changeset 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
files xmsannotator_advanced.xml
diffstat 1 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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>