diff matchms_similarity.xml @ 1:872d8040f713 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a

--- a/matchms_similarity.xml	Tue Jun 27 14:26:29 2023 +0000
+++ b/matchms_similarity.xml	Thu Oct 12 13:25:30 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="matchms_similarity" name="matchms similarity" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_similarity" name="matchms similarity" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>calculate the similarity score and matched peaks</description>
 
     <macros>
@@ -13,21 +13,21 @@
         <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
     </requirements>
 
-    <environment_variables>
-        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
-    </environment_variables>
-
     <command detect_errors="exit_code"><![CDATA[
         sh ${matchms_python_cli}
     ]]> </command>
 
+    <environment_variables>
+        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+    </environment_variables>
+
     <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" \
@@ -58,12 +58,15 @@
         <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."/>
             </when>
+            <when value="TRUE"></when>
         </conditional>
         <param label="Scores array type" name="array_type" type="select" display="radio"
                help="Matrix type for storing scores objects. Sparse type more memory-efficient and better for large arrays.
@@ -107,12 +110,15 @@
 
 
         <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."/>
             </when>
+            <when value="FALSE"></when>
         </conditional>
     </inputs>
 
@@ -141,7 +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">
@@ -164,7 +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"/>
@@ -178,7 +184,7 @@
                 <param name="model_weights" value="similarity/spec2vec/weights_100.binary" ftype="auto"/>
                 <param name="allow_missing_percentage" value="1.0"/>
             </conditional>
-            <output name="similarity_scores" file="similarity/scores_test6_out.json" ftype="json" compare="sim_size" delta="100000"/>
+            <output name="similarity_scores" file="similarity/scores_test6_out.json" ftype="json" compare="sim_size" delta="1000"/>
         </test>
     </tests>