Merge pull request #1 from paulzierep/maaslin2-renu

fix column name input

tools/maaslin2/maaslin2.xml

@@ -7,6 +7,29 @@
     <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" 
+## using awk so that the file is only parsed on command line execution
+
+#set idx = []
+#for $i in $fixed_effects:
+    #silent idx.append(f'${i}')
+#end for
+#set idx_for_awk = ','.join(idx)
+
+fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
+echo 'Assigned fixed effects as:' \$fixed_effects &&
+
+#set idx = []
+#for $i in $random_effects:
+    #silent idx.append(f'${i}')
+#end for
+#set idx_for_awk = ','.join(idx)
+
+random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
+echo 'Assigned random effects as:' \$random_effects &&
+
 ln -s '$input_data' 'input_data.tsv'
 &&
 ln -s '$input_metadata' 'input_metadata.tsv'
@@ -31,10 +54,10 @@ Maaslin2.R
     --analysis_method '$additional_options.analysis_method'
 #end if
 #if $random_effects
-    --random_effects '$random_effects'
+    --random_effects \$random_effects
 #end if
 #if $fixed_effects
-    --fixed_effects '$fixed_effects'
+    --fixed_effects \$fixed_effects
 #end if
 #if $additional_options.correction
     --correction '$additional_options.correction'
@@ -53,17 +76,12 @@ 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"/>