From 3918739c1e80a742cadd0734700eb8e7ee98c0b4 Mon Sep 17 00:00:00 2001
From: RENU <renu244pal@gmail.com>
Date: Wed, 27 Mar 2024 20:11:43 +0100
Subject: [PATCH 1/6] interaction:fixed effects and corrections modified

---
 tools/maaslin2/maaslin2.xml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index 1d319ae0155..ea8e471f49e 100644
--- a/tools/maaslin2/maaslin2.xml
+++ b/tools/maaslin2/maaslin2.xml
@@ -55,7 +55,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
     <inputs>
         <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
         <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
-        <param argument="--fixed_effects" type="select" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects">
+        <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>
@@ -87,7 +87,14 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
                 <option value="NEGBIN">NEGBIN</option>
                 <option value="ZINB">ZINB</option>
             </param>
-            <param argument="--correction" type="text" value="BH" optional="true" label="Correction" help="The correction method for computing  the q-value"/>
+            <param argument="--correction" type="select" value="BH" multiple="true" optional="true" label="Correction" help="The correction method for computing  the q-value">
+            <option value="holm">holm</option>
+            <option value="hochberg">hochberg</option>
+            <option value="hommel">hommel</option>
+            <option value="bonferroni">bonferroni</option>
+            <option value="BH">BH</option>
+            <option value="BY">BY</option>
+            </param>
             <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="--standardize FALSE" checked="true" label="Apply z-score so continuous metadata are on  the same scale"/>
         </section>          
         <section name="output" title="Set Plotting Output" expanded="true">

From 8fa089e385e81b008c5458df5df84a39df8e8f75 Mon Sep 17 00:00:00 2001
From: RENU <renu244pal@gmail.com>
Date: Wed, 17 Apr 2024 23:02:34 +0200
Subject: [PATCH 2/6] fixed effects, random effects , corrections methods
 modified and version bumped

---
 tools/maaslin2/maaslin2.xml | 68 +++++++++++++++++++++++++------------
 tools/maaslin2/macros.xml   |  4 +--
 2 files changed, 48 insertions(+), 24 deletions(-)

diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index ea8e471f49e..c56fe2308dd 100644
--- a/tools/maaslin2/maaslin2.xml
+++ b/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'
@@ -51,19 +74,17 @@ Maaslin2.R
     'outputFolder'
 &&
 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_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" 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" 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"/>
@@ -87,13 +108,13 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
                 <option value="NEGBIN">NEGBIN</option>
                 <option value="ZINB">ZINB</option>
             </param>
-            <param argument="--correction" type="select" value="BH" multiple="true" optional="true" label="Correction" help="The correction method for computing  the q-value">
-            <option value="holm">holm</option>
-            <option value="hochberg">hochberg</option>
-            <option value="hommel">hommel</option>
-            <option value="bonferroni">bonferroni</option>
-            <option value="BH">BH</option>
-            <option value="BY">BY</option>
+            <param argument="--correction" type="select" value="BH" multiple="true" optional="true" label="Correction" help="The correction method for computing  the q-value ">
+                <option value="holm">Holm</option>
+                <option value="hochberg">Hochberg</option>
+                <option value="hommel">Hommel</option>
+                <option value="bonferroni">Bonferroni</option>
+                <option value="BH">Benjamini-Hochberg(BH)</option>
+                <option value="BY">Benjamini-Yekutieli(BY)</option>
             </param>
             <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="--standardize FALSE" checked="true" label="Apply z-score so continuous metadata are on  the same scale"/>
         </section>          
@@ -122,8 +143,8 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="random_effects" value="site,subject"/>
-            <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age"/>
+            <param name="random_effects" value= "c2: site,c5: subject"/> 
+            <param name="fixed_effects" value="c4: diagnosis,c9: dysbiosisnonIBD,c10: dysbiosisUC,c11: dysbiosisCD,c6: antibiotics,c3: age"/> 
             <section name="additional_options">
                 <param name="min_abundance" value="0.0"/>
                 <param name="min_prevalence" value="0.1"/>
@@ -205,7 +226,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/>
+            <param name="fixed_effects" value="c4: diagnosis,c9: dysbiosisnonIBD"/>
             <section name="additional_options">
                 <param name="min_abundance" value="0.0"/>
                 <param name="min_prevalence" value="0.1"/>
@@ -252,7 +273,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/>
+            <param name="fixed_effects" value="c4: diagnosis,c9: dysbiosisnonIBD"/>
             <section name="additional_options">
                 <param name="min_abundance" value="0.0001"/>
                 <param name="min_prevalence" value="0.1"/>
@@ -354,6 +375,9 @@ Output
         - It only includes associations with q-values <= to the threshold.
     - Data frame with residuals for each feature (R data file)
         - This file contains a data frame with residuals for each feature.
+        
+Correction methods to compute the q-value : https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/p.adjust
+
 2- Visualization output files
     - Heatmap of the significant associations (PDF file)
         - This file contains a heatmap of the significant associations.
diff --git a/tools/maaslin2/macros.xml b/tools/maaslin2/macros.xml
index 7903f9f7018..335c4eca97a 100644
--- a/tools/maaslin2/macros.xml
+++ b/tools/maaslin2/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.99.12</token>
+    <token name="@TOOL_VERSION@">1.7.3</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="edam_ontology">
@@ -21,4 +21,4 @@
             <yield/>
         </requirements>
     </xml>
- </macros>
\ No newline at end of file
+ </macros>

From bfc500c276a8c39eeca5a8730c830266c901fcaa Mon Sep 17 00:00:00 2001
From: RENU <renu244pal@gmail.com>
Date: Fri, 19 Apr 2024 22:55:00 +0200
Subject: [PATCH 3/6] maaslin2: test cases added

---
 tools/maaslin2/maaslin2.xml | 105 ++++++++++++++++++++++++++++++++++--
 tools/maaslin2/macros.xml   |   2 +-
 2 files changed, 103 insertions(+), 4 deletions(-)

diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index c56fe2308dd..9b02af0511e 100644
--- a/tools/maaslin2/maaslin2.xml
+++ b/tools/maaslin2/maaslin2.xml
@@ -12,6 +12,7 @@
 ## can only return indices with type="data_column" 
 ## using awk so that the file is only parsed on command line execution
 
+#if $fixed_effects
 #set idx = []
 #for $i in $fixed_effects:
     #silent idx.append(f'${i}')
@@ -20,7 +21,10 @@
 
 fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
 echo 'Assigned fixed effects as:' \$fixed_effects &&
+#end if
+
 
+#if $random_effects
 #set idx = []
 #for $i in $random_effects:
     #silent idx.append(f'${i}')
@@ -29,6 +33,7 @@ echo 'Assigned fixed effects as:' \$fixed_effects &&
 
 random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
 echo 'Assigned random effects as:' \$random_effects &&
+#end if
 
 ln -s '$input_data' 'input_data.tsv'
 &&
@@ -79,9 +84,9 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
     <inputs>
         <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
         <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
-        <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true"  multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed 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" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects, Default value: All " />
         		
-        <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Random effects" help="The random 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" label="Random effects" help="The random effects for the model,  comma-delimited for multiple effects, Default: None" />
         	
        
         	
@@ -108,7 +113,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
                 <option value="NEGBIN">NEGBIN</option>
                 <option value="ZINB">ZINB</option>
             </param>
-            <param argument="--correction" type="select" value="BH" multiple="true" optional="true" label="Correction" help="The correction method for computing  the q-value ">
+            <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing  the q-value ">
                 <option value="holm">Holm</option>
                 <option value="hochberg">Hochberg</option>
                 <option value="hommel">Hommel</option>
@@ -332,6 +337,100 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
                 </element>                                                                    
             </output_collection>
         </test>   
+        <test expect_num_outputs="5">
+            <param name="input_data" value="HMP2_taxonomy.tsv"/>
+            <param name="input_metadata" value="HMP2_metadata.tsv"/>
+            <param name="random_effects" value="c3: age" />
+            <section name="additional_options">
+                <param name="min_abundance" value="0.0"/>
+                <param name="min_prevalence" value="0.1"/>
+                <param name="max_significance" value="0.25"/>
+                <param name="normalization" value="TSS"/>
+                <param name="transform" value="LOG"/>
+                <param name="analysis_method" value="LM"/>
+                <param name="correction" value="BY"/>
+                <param name="standardize" value="True"/>
+            </section>
+            <section name="output">
+                <param name="plot_heatmap" value="true"/>
+                <param name="heatmap_first_n" value="50"/>
+                <param name="plot_scatter" value="true"/>
+                <param name="residuals_output" value="true"/>
+            </section>
+            <output name="all_results">
+                <assert_contents>
+                    <has_text text="feature"/>
+                    <has_n_lines n="8092"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
+            <output name="significant_results">
+                <assert_contents>
+                    <has_text text="subject"/>
+                    <has_n_lines n="213"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
+            <output name="residuals">
+                <assert_contents>
+                    <has_size value="671142" delta="1000"/>
+                </assert_contents>
+            </output>
+            <output_collection name="figures_pdfs" type="list">
+                <element name="heatmap.pdf" ftype="pdf">
+                    <assert_contents>
+                        <has_size value="7000" delta="1000" />
+                    </assert_contents>
+                </element>                                                              
+            </output_collection>
+        </test> 
+        <test expect_num_outputs="5">
+            <param name="input_data" value="HMP2_taxonomy.tsv"/>
+            <param name="input_metadata" value="HMP2_metadata.tsv"/>
+           
+            <section name="additional_options">
+                <param name="min_abundance" value="0.0"/>
+                <param name="min_prevalence" value="0.1"/>
+                <param name="max_significance" value="0.25"/>
+                <param name="normalization" value="TSS"/>
+                <param name="transform" value="LOG"/>
+                <param name="analysis_method" value="LM"/>
+                <param name="correction" value="BH"/>
+                <param name="standardize" value="True"/>
+            </section>
+            <section name="output">
+                <param name="plot_heatmap" value="true"/>
+                <param name="heatmap_first_n" value="50"/>
+                <param name="plot_scatter" value="true"/>
+                <param name="residuals_output" value="true"/>
+            </section>
+            <output name="all_results">
+                <assert_contents>
+                    <has_text text="feature"/>
+                    <has_n_lines n="8092"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
+            <output name="significant_results">
+                <assert_contents>
+                    <has_text text="subject"/>
+                    <has_n_lines n="880"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
+            <output name="residuals">
+                <assert_contents>
+                    <has_size value="670759" delta="1000"/>
+                </assert_contents>
+            </output>
+            <output_collection name="figures_pdfs" type="list">
+                <element name="heatmap.pdf" ftype="pdf">
+                    <assert_contents>
+                        <has_size value="7900" delta="1000" />
+                    </assert_contents>
+                </element>                                                              
+            </output_collection>
+        </test> 
     </tests>
     <help><![CDATA[
 @HELP_HEADER@
diff --git a/tools/maaslin2/macros.xml b/tools/maaslin2/macros.xml
index 335c4eca97a..b9646d382df 100644
--- a/tools/maaslin2/macros.xml
+++ b/tools/maaslin2/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.7.3</token>
+    <token name="@TOOL_VERSION@">0.99.12</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="edam_ontology">

From 02ab4b6ef3b41f1eda8fd6e7a6f1652f3fb2ba5f Mon Sep 17 00:00:00 2001
From: RENU <renu244pal@gmail.com>
Date: Wed, 24 Apr 2024 19:46:29 +0200
Subject: [PATCH 4/6] maaslin2 : updated fixed and random effects to include
 just numbers in tests

---
 tools/maaslin2/maaslin2.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index 9b02af0511e..fa5a9f220d2 100644
--- a/tools/maaslin2/maaslin2.xml
+++ b/tools/maaslin2/maaslin2.xml
@@ -148,8 +148,8 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="random_effects" value= "c2: site,c5: subject"/> 
-            <param name="fixed_effects" value="c4: diagnosis,c9: dysbiosisnonIBD,c10: dysbiosisUC,c11: dysbiosisCD,c6: antibiotics,c3: age"/> 
+            <param name="random_effects" value= "2,5"/> 
+            <param name="fixed_effects" value="4,9,10,11,6,3"/> 
             <section name="additional_options">
                 <param name="min_abundance" value="0.0"/>
                 <param name="min_prevalence" value="0.1"/>
@@ -231,7 +231,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="fixed_effects" value="c4: diagnosis,c9: dysbiosisnonIBD"/>
+            <param name="fixed_effects" value="4,9"/>
             <section name="additional_options">
                 <param name="min_abundance" value="0.0"/>
                 <param name="min_prevalence" value="0.1"/>
@@ -278,7 +278,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="fixed_effects" value="c4: diagnosis,c9: dysbiosisnonIBD"/>
+            <param name="fixed_effects" value="4,9"/>
             <section name="additional_options">
                 <param name="min_abundance" value="0.0001"/>
                 <param name="min_prevalence" value="0.1"/>
@@ -340,7 +340,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="random_effects" value="c3: age" />
+            <param name="random_effects" value="3" />
             <section name="additional_options">
                 <param name="min_abundance" value="0.0"/>
                 <param name="min_prevalence" value="0.1"/>

From 18bb723dfe440474b55b54f14d05894942ed5d4f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 25 Apr 2024 14:55:00 +0200
Subject: [PATCH 5/6] Update tools/maaslin2/maaslin2.xml

---
 tools/maaslin2/maaslin2.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index fa5a9f220d2..67265b3f453 100644
--- a/tools/maaslin2/maaslin2.xml
+++ b/tools/maaslin2/maaslin2.xml
@@ -367,7 +367,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
             <output name="significant_results">
                 <assert_contents>
                     <has_text text="subject"/>
-                    <has_n_lines n="213"/>
+                    <has_n_lines n="216" delta="5"/>
                     <has_n_columns n="9"/>
                 </assert_contents>
             </output>

From 621439a832cac1a6ed4f860eb9dc54b2e25f55c9 Mon Sep 17 00:00:00 2001
From: RENU <renu244pal@gmail.com>
Date: Fri, 26 Apr 2024 14:45:16 +0200
Subject: [PATCH 6/6] maaslin2: update correction help

---
 tools/maaslin2/maaslin2.xml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index 67265b3f453..dbed38104d6 100644
--- a/tools/maaslin2/maaslin2.xml
+++ b/tools/maaslin2/maaslin2.xml
@@ -113,11 +113,8 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
                 <option value="NEGBIN">NEGBIN</option>
                 <option value="ZINB">ZINB</option>
             </param>
-            <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing  the q-value ">
-                <option value="holm">Holm</option>
-                <option value="hochberg">Hochberg</option>
-                <option value="hommel">Hommel</option>
-                <option value="bonferroni">Bonferroni</option>
+            <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing  the q-value, Default: BH ">
+                
                 <option value="BH">Benjamini-Hochberg(BH)</option>
                 <option value="BY">Benjamini-Yekutieli(BY)</option>
             </param>