# HG changeset patch
# User recetox
# Date 1635936840 0
# Node ID c6800346a5a8eacad8c92d746d31362ec34ef018
# Parent  a48e50d1dba31f560b567bed48a508b10b9ded9c
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 330dd8c8be0c43b5ce38d8c5573325b2c555491d"

diff -r a48e50d1dba3 -r c6800346a5a8 october_recetox_xmsannotator_advanced.xml
--- a/october_recetox_xmsannotator_advanced.xml	Tue Nov 02 14:40:12 2021 +0000
+++ b/october_recetox_xmsannotator_advanced.xml	Wed Nov 03 10:54:00 2021 +0000
@@ -17,7 +17,7 @@
             #if $peak_table.is_of_type("parquet")
                 peak_table = load_peak_table_parquet("${peak_table}"),
             #end if
-            ## adduct_table = load_adduct_table_parquet("${adduct_table}"),
+                adduct_table = load_adduct_table_parquet("${adduct_table}"),
                 adduct_weights = as.data.frame(read.csv("${adduct_weights}")),
                 compound_table = load_compound_table_parquet("${compound_table}"),
                 mass_tolerance = 1e-6 * ${mass_tolerance_ppm},
@@ -26,15 +26,8 @@
                 min_cluster_size = as.integer($clustering.min_cluster_size),
                 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}"),
-            ## #end if
-            ## #if $scoring.boost_compounds
-            ##     boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds}"),
-            ## #end if
                 redundancy_filtering = $scoring.redundancy_filtering,
                 n_workers = n_workers,
-            ## new params
                 intensity_deviation_tolerance = as.double($intensity_deviation_tolerance),
                 mass_defect_tolerance = as.double($mass_defect_tolerance),
                 mass_defect_precision = as.double($mass_defect_precision),
@@ -43,7 +36,6 @@
                 min_ions_per_chemical = as.integer($min_ions_per_chemical),
                 filter_by = "$filter_by"
             )
-
             save_parquet(data = annotation, file = "${annotation_parquet}")
         ]]></configfile>
     </configfiles>
@@ -59,10 +51,6 @@
             </param>
         </expand>
         <section name="clustering" title="Clustering">
-            <param name="correlation_method" type="select" display="radio" label="Correlation method">
-                <option value="pearson" selected="true"/>
-                <option value="spearman"/>
-            </param>
             <param name="correlation_threshold" type="float" value="0.7">
                 <label>Correlation threshold</label>
                 <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help>
@@ -84,8 +72,8 @@
                     Network type parameter affects how the network's adjacency matrix is created from the correlation
                     matrix (see WGCNA package documentation).
                 </help>
-                <option value="signed"/>
-                <option value="unsigned" selected="true"/>
+                <option value="signed">Signed</option>
+                <option value="unsigned" selected="true">Unsigned</option>
             </param>
         </section>
         <section name="scoring" title="Scoring" expanded="true">
@@ -96,22 +84,6 @@
                     cluster. Otherwise, do not account for cluster membership.
                 </help>
             </param>
-            <!-- <param name="expected_adducts" type="data" format="csv" optional="true">
-                <label>Expected adducts (optional)</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>
-            </param> -->
-            <!-- <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>
-            </param> -->
             <param name="min_isp" type="integer" min="0" value="1">
                 <label>Minimum number of expected isotopes</label>
                 <help>