update

tools/maaslin2/maaslin2.xml

@@ -10,24 +10,25 @@
 
 ## 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
 
-## get header
-#set $input = open(str($input_metadata), 'r')
-#set $header = $input.readlines()[0].split('\t')
-
-## get fixed effects
-#set $fixed_effects_val = []
+#set idx = []
 #for $i in $fixed_effects:
-    #silent $fixed_effects_val.append($header[int($i)])
+    #silent idx.append(f'${i}')
 #end for
-#set $fixed_effects = ','.join($fixed_effects_val)
+#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 &&
 
-## get random effects
-#set $random_effects_val = []
+#set idx = []
 #for $i in $random_effects:
-    #silent $random_effects_val.append($header[int($i)])
+    #silent idx.append(f'${i}')
 #end for
-#set $random_effects = ','.join($random_effects_val)
+#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 '$input_data' 'input_data.tsv'
 &&
@@ -53,10 +54,10 @@ Maaslin2.R
     --analysis_method '$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'