diff wormsmeasurements.xml @ 1:6f75ab89587a draft default tip

planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c

--- a/wormsmeasurements.xml	Wed May 14 15:08:00 2025 +0000
+++ b/wormsmeasurements.xml	Wed May 28 10:13:42 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="WormsMeasurements" name="Enrich dataset with WoRMS" version="0.1.1" profile="23.2">
+<tool id="WormsMeasurements" name="Enrich dataset with WoRMS" version="0.1.2" profile="23.2">
     <description>Enrich dataset with measurement type data from WoRMS</description>
 
     <requirements>
@@ -16,15 +16,20 @@
     '$scientic_name'
     '$include_inherited'
     '$pivot_wider'
+    '$exclude_NA'
     '$output'
     ]]></command>
 
     <inputs>
         <param name="data" type="data" format="tabular" label="occurrence data"/>
-        <param name="measurement_types" type="text" format="txt" label="list of measurement types"/>
-        <param name="scientic_name" type="text" format="txt" label="scientific names column name" value="scientificName"/>
+        <param name="measurement_types" type="text" format="txt" label="list of measurement types">
+        </param>
+        <param name="scientic_name" type="text" format="txt" label="scientific names column name" value="scientificName" optional="false">
+            <validator type="regex" message="this field can't be empty">.+</validator>
+        </param>
         <param name="include_inherited" type="boolean" label="include attributes inherited from parent taxon" checked="false"/>        
         <param name="pivot_wider" type="boolean" label="one hot encoding on the measurement types" checked="false"/>
+        <param name="exclude_NA" type="boolean" label="exclude lines with missing values (NA)" checked="false"/>
     </inputs>
 
     <outputs>
@@ -34,26 +39,29 @@
     <tests>
         <test>
             <param name="data" value="sample.tabular"/>
-            <param name="measurement_types" value="Development, Fecundity"/>
+            <param name="measurement_types" value="Development,Fecundity"/>
             <param name="scientic_name" value="scientificName"/>
             <param name="include_inherited" value="true"/>
             <param name="pivot_wider" value="false"/>
+            <param name="exclude_NA" value="false"/>
             <output name="output" file="enriched_data_inherited.tabular"/>
         </test>
         <test>
             <param name="data" value="sample.tabular"/>
-            <param name="measurement_types" value="Development, Fecundity"/>
+            <param name="measurement_types" value="Development,Fecundity"/>
             <param name="scientic_name" value="scientificName"/>
             <param name="include_inherited" value="false"/>
             <param name="pivot_wider" value="false"/>
+            <param name="exclude_NA" value="false"/>
             <output name="output" file="enriched_data.tabular"/>
         </test>
         <test>
             <param name="data" value="sample.tabular"/>
-            <param name="measurement_types" value="Development, Fecundity"/>
+            <param name="measurement_types" value="Development,Fecundity"/>
             <param name="include_inherited" value="true"/>
             <param name="scientic_name" value="scientificName"/>
             <param name="pivot_wider" value="true"/>
+            <param name="exclude_NA" value="false"/>
             <output name="output" file="enriched_data_inherited_ohe.tabular"/>
         </test>
     </tests>
@@ -76,6 +84,7 @@
 - **scientific names column name**: the name of column in the dataset containing scientific names.
 - **include attributes inherited from parent taxon**: usefull when the data you are looking for are incomplete.
 - **one hot encoding on the measurement types**: each possible values of a measurementType becomes a column encoded in 0/1
+- **exclude_NA**: exclude lines with missing measurement value
 
 ## Outputs: