From 3b25dba4e341b1cf89a0194cd42009c47eceb574 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Mon, 25 Sep 2023 15:31:47 +0200
Subject: [PATCH] changed boolean to select

---
 tools/matchms/macros.xml                      |  12 ++-
 tools/matchms/matchms_filtering.xml           | 100 +++++++-----------
 tools/matchms/matchms_similarity.xml          |  20 ++--
 tools/matchms/matchms_spectral_similarity.xml |   2 +-
 4 files changed, 58 insertions(+), 76 deletions(-)

diff --git a/tools/matchms/macros.xml b/tools/matchms/macros.xml
index 8beccdc2..83a1a8c5 100644
--- a/tools/matchms/macros.xml
+++ b/tools/matchms/macros.xml
@@ -57,9 +57,11 @@
 
     <xml name="input_param">
         <conditional name="scores">
-            <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE"
-                   checked="false"/>
-            <when value="TRUE">
+            <param name="use_scores" label="Use Scores Object" type="select">
+                <option value="False" selected="true">FALSE</option>
+                <option value="True">TRUE</option>
+            </param>
+            <when value="True">
                 <param label="Scores object" name="scores_in" type="data" format="json"
                     help="Scores objects calculated previously using one of the matchms similarity tools." />
                 <param label="join type" name="join_type" type="select" display="radio"
@@ -70,7 +72,7 @@
                     <option value="outer">outer</option>
                 </param>
             </when>
-            <when value="FALSE">
+            <when value="False">
                 <param label="Queries spectra" name="queries" type="data" format="msp"
                     help="Query mass spectra to match against references."/>
                 <param label="Reference spectra" name="references" type="data" format="msp"
@@ -89,7 +91,7 @@
 <token name="@init_scores@">
 from matchms.importing import load_from_msp, scores_from_json
 from matchms import Scores
-#if $scores.use_scores
+#if $scores.use_scores == "True"
 scores = scores_from_json("$scores_in")
 join_type = "$scores.join_type"
 #else
diff --git a/tools/matchms/matchms_filtering.xml b/tools/matchms/matchms_filtering.xml
index 1a3b7a71..cd70c028 100644
--- a/tools/matchms/matchms_filtering.xml
+++ b/tools/matchms/matchms_filtering.xml
@@ -30,32 +30,32 @@
             python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
             --spectra "$spectra" \
             --spectra_format "$spectra.ext" \
-            #if $normalise_intensities.is_true
+            #if $normalise_intensities_is_true == "TRUE"
                 -normalise_intensities \
             #end if
-            #if $default_filters.is_true
+            #if $default_filters_is_true == "TRUE"
                 -default_filters \
             #end if
-            #if $clean_metadata.is_true
+            #if $clean_metadata_is_true == "TRUE"
                 -clean_metadata \
             #end if
-            #if $relative_intensity.is_true
+            #if $relative_intensity.is_true == "TRUE"
                 -relative_intensity \
                 --from_intensity "$relative_intensity.from_intensity" \
                 --to_intensity "$relative_intensity.to_intensity" \
             #end if
-            #if $mz_range.is_true
+            #if $mz_range.is_true == "TRUE"
                 -mz_range \
                 --from_mz "$mz_range.from_mz" \
                 --to_mz "$mz_range.to_mz" \
             #end if
-            #if $require_smiles.is_true
+            #if $require_smiles_is_true == "TRUE"
                 -require_smiles \
             #end if
-            #if $require_inchi.is_true
+            #if $require_inchi_is_true == "TRUE"
                 -require_inchi \
             #end if
-            #if $reduce_to_top_n_peaks.is_true
+            #if $reduce_to_top_n_peaks.is_true == "TRUE"
                 -reduce_to_top_n_peaks \
                 --n_max "$reduce_to_top_n_peaks.n_max" \
             #end if
@@ -65,31 +65,19 @@
 
     <inputs>
         <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />
-
-        <conditional name="normalise_intensities">
-            <param name="is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
-                   help="Normalize intensities of peaks (and losses) to unit height."/>
-            <when value="TRUE"></when>
-            <when value="FALSE"></when>
-        </conditional>
-
-        <conditional name="default_filters">
-            <param name="is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
-                   help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
-            <when value="TRUE"></when>
-            <when value="FALSE"></when>
-        </conditional>
-
-        <conditional name="clean_metadata">
-            <param name="is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
-                   help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
-            <when value="TRUE"></when>
-            <when value="FALSE"></when>
-        </conditional>
+        <param name="normalise_intensities_is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
+                help="Normalize intensities of peaks (and losses) to unit height."/>
+        <param name="default_filters_is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
+                help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
+        <param name="clean_metadata_is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
+                help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
 
         <conditional name="relative_intensity">
-            <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
-                   help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." />
+            <param name="is_true" label="Filter relative intensity" type="select" 
+                   help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum).">
+                <option value="FALSE" selected="true">FALSE</option>
+                <option value="TRUE">TRUE</option>
+            </param>
             <when value="TRUE">
                 <param label="Minimum intensity" name="from_intensity" value="0" type="float" help="Lower bound for intensity filter." />
                 <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." />
@@ -98,8 +86,11 @@
         </conditional>
 
         <conditional name="mz_range">
-            <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
-                   help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)." />
+            <param name="is_true" label="Filter m/z range" type="select"
+                   help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum).">
+                <option value="FALSE" selected="true">FALSE</option>
+                <option value="TRUE">TRUE</option>
+            </param>
             <when value="TRUE">
                 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
                 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
@@ -107,23 +98,18 @@
             <when value="FALSE"></when>
         </conditional>
 
-        <conditional name="require_smiles">
-            <param name="is_true" label="Require SMILES" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
-                   help="Remove spectra that does not contain SMILES." />
-            <when value="TRUE"></when>
-            <when value="FALSE"></when>
-        </conditional>
+        <param name="require_smiles_is_true" label="Require SMILES" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
+                help="Remove spectra that does not contain SMILES." />
 
-        <conditional name="require_inchi">
-            <param name="is_true" label="Require INCHI" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
-                   help="Remove spectra that does not contain INCHI." />
-            <when value="TRUE"></when>
-            <when value="FALSE"></when>
-        </conditional>
+        <param name="require_inchi_is_true" label="Require INCHI" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
+                help="Remove spectra that does not contain INCHI." />
 
         <conditional name="reduce_to_top_n_peaks">
-            <param name="is_true" label="Reduce to top n peaks" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
-                   help="Lowest intensity peaks will be removed when it has more peaks than desired." />
+            <param name="is_true" label="Reduce to top n peaks" type="select"
+                   help="Lowest intensity peaks will be removed when it has more peaks than desired.">
+                <option value="FALSE" selected="true">FALSE</option>
+                <option value="TRUE">TRUE</option>
+            </param>
             <when value="TRUE">
                 <param label="Maximum number of peaks" name="n_max" value="5" type="integer" help="Maximum number of peaks. Remove peaks if more peaks are found." />
             </when>
@@ -139,23 +125,17 @@
     <tests>
         <test>
             <param name="spectra" value="filtering/input.msp" ftype="msp"/>
-            <section name="normalise_intensities">
-                <param name="is_true" value="TRUE"/>
-            </section>
+            <param name="normalise_intensities_is_true" value="TRUE"/>
             <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/>
         </test>
         <test>
             <param name="spectra" value="filtering/input.msp" ftype="msp"/>
-            <section name="default_filters">
-                <param name="is_true" value="TRUE"/>
-            </section>
+            <param name="default_filters_is_true" value="TRUE"/>
             <output name="output" file="filtering/default_filters.msp" ftype="msp"/>
         </test>
         <test>
             <param name="spectra" value="filtering/input.msp" ftype="msp"/>
-            <section name="clean_metadata">
-                <param name="is_true" value="TRUE"/>
-            </section>
+            <param name="clean_metadata_is_true" value="TRUE"/>
             <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/>
         </test>
         <test>
@@ -178,16 +158,12 @@
         </test>
         <test>
             <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
-            <section name="require_smiles">
-                <param name="is_true" value="TRUE"/>
-            </section>
+            <param name="require_smiles_is_true" value="TRUE"/>
             <output name="output" file="filtering/require_smiles_out.msp" ftype="msp"/>
         </test>
         <test>
             <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
-            <section name="require_inchi">
-                <param name="is_true" value="TRUE"/>
-            </section>
+            <param name="require_inchi_is_true" value="TRUE"/>
             <output name="output" file="filtering/require_inchi_out.msp" ftype="msp"/>
         </test>
         <test>
diff --git a/tools/matchms/matchms_similarity.xml b/tools/matchms/matchms_similarity.xml
index c827f1fa..d196f0ff 100644
--- a/tools/matchms/matchms_similarity.xml
+++ b/tools/matchms/matchms_similarity.xml
@@ -24,10 +24,10 @@
     <configfiles>
         <configfile name="matchms_python_cli">
             python3 ${__tool_directory__}/matchms_similarity_wrapper.py \
-            #if $ri_filtering.is_true
+            #if $ri_filtering.is_true == "TRUE"
             -r $ri_filtering.tolerance \
             #end if
-            #if $symmetric.is_symmetric
+            #if $symmetric.is_symmetric == "TRUE"
             -s \
             #else
             --ref "$references" \
@@ -58,8 +58,10 @@
         <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
                help="Query mass spectra to match against references."/>
         <conditional name="symmetric">
-            <param name="is_symmetric" label="Symmetric" type="boolean" truevalue="TRUE" falsevalue="FALSE"
-                   checked="false"/>
+            <param name="is_symmetric" label="Symmetric" type="select">
+                <option value="FALSE" selected="true">FALSE</option>
+                <option value="TRUE">TRUE</option>
+            </param>
             <when value="FALSE">
                 <param label="Reference spectra" name="references" type="data" format="msp,mgf"
                        help="Reference mass spectra to match against as library."/>
@@ -108,8 +110,10 @@
 
 
         <conditional name="ri_filtering">
-            <param name="is_true" label="Apply RI filtering" type="boolean" truevalue="TRUE" falsevalue="FALSE"
-                   checked="false"/>
+            <param name="is_true" label="Apply RI filtering" type="select">
+                <option value="FALSE" selected="true">FALSE</option>
+                <option value="TRUE">TRUE</option>
+            </param>
             <when value="TRUE">
                 <param label="tolerance" name="tolerance" type="float" value="60"
                        help="Peaks will be considered a match when less than tolerance apart."/>
@@ -143,7 +147,7 @@
             <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
             <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
             <conditional name="ri_filtering">
-                <param name="is_true" value="True"></param>
+                <param name="is_true" value="TRUE"></param>
                 <param name="tolerance" value="60.0" />
             </conditional>
             <conditional name="metric">
@@ -166,7 +170,7 @@
             </conditional>
             <param name="is_symmetric" value="TRUE" />
             <conditional name="ri_filtering">
-                <param name="is_true" value="True"></param>
+                <param name="is_true" value="TRUE"></param>
                 <param name="tolerance" value="60.0" />
             </conditional>
             <output name="similarity_scores" file="similarity/scores_test5_out.json" ftype="json"/>
diff --git a/tools/matchms/matchms_spectral_similarity.xml b/tools/matchms/matchms_spectral_similarity.xml
index 12dc1bde..d0d9c82e 100644
--- a/tools/matchms/matchms_spectral_similarity.xml
+++ b/tools/matchms/matchms_spectral_similarity.xml
@@ -36,7 +36,7 @@ name="${similarity_metric}_${algorithm.tolerance}_${algorithm.mz_power}_${algori
 
 @init_scores@
 
-#if $scores.use_scores
+#if $scores.use_scores == "True"
 layer = similarity.sparse_array(
     references=scores.references,
     queries=scores.queries,