From 0024dfd7d3629aaf16c88d08bb2b8cd5c91c4bd0 Mon Sep 17 00:00:00 2001
From: paulzierep <paul.zierep@googlemail.com>
Date: Tue, 16 Apr 2024 10:56:52 +0200
Subject: [PATCH 1/2] fix column name input

---
 tools/maaslin2/maaslin2.xml | 37 +++++++++++++++++++++++++++----------
 1 file changed, 27 insertions(+), 10 deletions(-)

diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index 51c1fdee756..40c1b1a4ede 100644
--- a/tools/maaslin2/maaslin2.xml
+++ b/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"/>

From d3e43dae4e1d018767bb3199019242420cb97a90 Mon Sep 17 00:00:00 2001
From: paulzierep <paul.zierep@googlemail.com>
Date: Tue, 16 Apr 2024 12:27:48 +0200
Subject: [PATCH 2/2] update

---
 tools/maaslin2/maaslin2.xml | 29 +++++++++++++++--------------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index 40c1b1a4ede..01b209e6e46 100644
--- a/tools/maaslin2/maaslin2.xml
+++ b/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'