fix column name input

tools/maaslin2/maaslin2.xml

@@ -7,6 +7,28 @@
     <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
+
+## get column names of fixed and random effect from the input file, since galaxy 
+## can only return indices with type="data_column" 
+
+## get header
+#set $input = open(str($input_metadata), 'r')
+#set $header = $input.readlines()[0].split('\t')
+
+## get fixed effects
+#set $fixed_effects_val = []
+#for $i in $fixed_effects:
+    #silent $fixed_effects_val.append($header[int($i)])
+#end for
+#set $fixed_effects = ','.join($fixed_effects_val)
+
+## get random effects
+#set $random_effects_val = []
+#for $i in $random_effects:
+    #silent $random_effects_val.append($header[int($i)])
+#end for
+#set $random_effects = ','.join($random_effects_val)
+
 ln -s '$input_data' 'input_data.tsv'
 &&
 ln -s '$input_metadata' 'input_metadata.tsv'
@@ -53,17 +75,12 @@ Maaslin2.R
 cd outputFolder && mkdir -p figures/ && cp *.pdf figures
     ]]></command>
     <inputs>
-        <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
+        <param name="input_data" type="data" format="tsv" label="Data (or features) file"/>
         <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
-        <param argument="--fixed_effects" type="text" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects">
-            <option value="diagnosis" selected="true">diagnosis</option>
-            <option value="dysbiosisnonIBD" selected="true">dysbiosisnonIBD</option>
-            <option value="dysbiosisUC" selected="true">dysbiosisUC</option>
-            <option value="dysbiosisCD" selected="true">dysbiosisCD</option>
-            <option value="antibiotics" selected="true">antibiotics</option>
-            <option value="age" selected="true">age</option>
-        </param>        
-        <param argument="--random_effects" type="text" multiple="true" optional="true" label="Random effects" help="The random effects for the model,  comma-delimited for multiple effects"/>        
+
+        <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" numerical="false" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects" />
+        <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" numerical="false" label="Random effects" help="The random effects for the model,  comma-delimited for multiple effects" />
+
         <section name="additional_options" title="Additional Options" expanded="true">
             <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/>
             <param argument="--min_prevalence" type="float" value="0.1" optional="true" label="Minimum prevalence" help="The minimum percent of samples for which a feature is detected at minimum abundance"/>