From 972ab779017f8c80c35db46c3ec9c818982c2778 Mon Sep 17 00:00:00 2001
From: mthang <mthang@qfab.org>
Date: Tue, 12 Nov 2024 08:02:27 +0000
Subject: [PATCH 1/5] patch krakentools beta_diversity.xml

---
 tools/krakentools/beta_diversity.xml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/krakentools/beta_diversity.xml b/tools/krakentools/beta_diversity.xml
index 59539b66b58..3570e4fa35b 100644
--- a/tools/krakentools/beta_diversity.xml
+++ b/tools/krakentools/beta_diversity.xml
@@ -7,10 +7,14 @@
     <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
+#for $input in $inputs
+	ln -s '$input' '${input.element_identifier}' &&
+#end for
+
 beta_diversity.py 
     --inputs
     #for $input in $inputs 
-        '$input' 
+	'${input.element_identifier}' 
     #end for
     --type '$sample.type'
     #if $sample.type == 'kreport'

From 4f9dac26744989bb780a34dde43219265589b71b Mon Sep 17 00:00:00 2001
From: mthang <mthang@qfab.org>
Date: Wed, 13 Nov 2024 05:19:38 +0000
Subject: [PATCH 2/5] add re.sub to beta_diversity.xml

---
 tools/krakentools/beta_diversity.xml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/tools/krakentools/beta_diversity.xml b/tools/krakentools/beta_diversity.xml
index 3570e4fa35b..caed10e7e6d 100644
--- a/tools/krakentools/beta_diversity.xml
+++ b/tools/krakentools/beta_diversity.xml
@@ -7,14 +7,19 @@
     <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
+#import re
+#set input_names=[]
+
 #for $input in $inputs
-	ln -s '$input' '${input.element_identifier}' &&
+	#set identifier = re.sub('[^\s\w\-\\.]', '_', str($input.element_identifier))
+	#silent $input_names.append($identifier)
+	ln -s '$input' '${identifier}' &&
 #end for
 
 beta_diversity.py 
     --inputs
-    #for $input in $inputs 
-	'${input.element_identifier}' 
+    #for $input_name in $input_names
+	'${input_name}' 
     #end for
     --type '$sample.type'
     #if $sample.type == 'kreport'

From 25b1b4170280bbb885b4ca0c72a2f5b389efb08e Mon Sep 17 00:00:00 2001
From: mthang <mthang@qfab.org>
Date: Fri, 15 Nov 2024 04:46:55 +0000
Subject: [PATCH 3/5] patch beta_diversity.xml

---
 tools/krakentools/beta_diversity.xml | 5 ++++-
 tools/krakentools/macros.xml         | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/tools/krakentools/beta_diversity.xml b/tools/krakentools/beta_diversity.xml
index caed10e7e6d..68e4908ee60 100644
--- a/tools/krakentools/beta_diversity.xml
+++ b/tools/krakentools/beta_diversity.xml
@@ -59,7 +59,10 @@ beta_diversity.py
             <param name="inputs" value="beta_bracken_1.tabular,beta_bracken_2.tabular,beta_bracken_3.tabular"/>
             <param name="type" value="bracken"/>
             <output name="output" ftype="txt">
-                <assert_contents>
+		 <assert_contents>
+		    <has_text text="beta_bracken_1.tabular"/>
+		    <has_text text="beta_bracken_2.tabular"/>
+		    <has_text text="beta_bracken_3.tabular"/>
                     <has_text text="0.629"/>
                     <has_text text="0.993"/>
                     <has_text text="0.995"/>
diff --git a/tools/krakentools/macros.xml b/tools/krakentools/macros.xml
index 0ae9832f810..84bf1f12c30 100644
--- a/tools/krakentools/macros.xml
+++ b/tools/krakentools/macros.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.2</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
         <xrefs>

From 5816c1f5fae2fece7d8dff48e4eedfb2636bc195 Mon Sep 17 00:00:00 2001
From: mthang <mthang@qfab.org>
Date: Fri, 15 Nov 2024 05:03:47 +0000
Subject: [PATCH 4/5] update test unit in beta_diversity.xml

---
 tools/krakentools/beta_diversity.xml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tools/krakentools/beta_diversity.xml b/tools/krakentools/beta_diversity.xml
index 68e4908ee60..5d5ab9b63e4 100644
--- a/tools/krakentools/beta_diversity.xml
+++ b/tools/krakentools/beta_diversity.xml
@@ -73,7 +73,10 @@ beta_diversity.py
             <param name="inputs" value="beta_kreport_1.tabular,beta_kreport_2.tabular,beta_kreport_3.tabular"/>
             <param name="type" value="kreport"/>
             <output name="output" ftype="txt">
-                <assert_contents>
+		 <assert_contents>
+                    <has_text text="beta_kreport_1.tabular"/>
+                    <has_text text="beta_kreport_2.tabular"/>
+                    <has_text text="beta_kreport_3.tabular"/>
                     <has_text text="0.584"/>
                     <has_text text="0.996"/>
                     <has_text text="0.995"/>
@@ -85,7 +88,9 @@ beta_diversity.py
             <param name="type" value="krona"/>
             <param name="level" value="G"/>
             <output name="output" ftype="txt">
-                <assert_contents>        
+		<assert_contents>
+		    <has_text text="beta_krona_1.tabular"/>
+		    <has_text text="beta_krona_2.tabular"/>
                     <has_text text="0.993"/>
                 </assert_contents>
             </output>

From ad1217d87c477ccbfc949a7edd7761313684ae4e Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 15 Nov 2024 11:51:53 +0100
Subject: [PATCH 5/5] make output tabular and improve assertions

---
 tools/krakentools/alpha_diversity.xml |  6 ++---
 tools/krakentools/beta_diversity.xml  | 34 +++++++++++++--------------
 2 files changed, 18 insertions(+), 22 deletions(-)

diff --git a/tools/krakentools/alpha_diversity.xml b/tools/krakentools/alpha_diversity.xml
index bd40ce7b7a1..da0fe3c8d64 100644
--- a/tools/krakentools/alpha_diversity.xml
+++ b/tools/krakentools/alpha_diversity.xml
@@ -4,9 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="biotools"/>
-    <expand macro="requirements">
-        <requirement type="package" version="1.9.3">scipy</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
 alpha_diversity.py 
@@ -33,7 +31,7 @@ alpha_diversity.py
             <param name="alpha" value="Sh"/>
             <output name="output" ftype="txt">
                 <assert_contents>
-                    <has_text text="Shannon's diversity: 4.194127607417342"/>
+                    <has_text text="Shannon's diversity: 4.194127607417341"/>
                 </assert_contents>
             </output>
         </test>
diff --git a/tools/krakentools/beta_diversity.xml b/tools/krakentools/beta_diversity.xml
index 5d5ab9b63e4..84dc552d361 100644
--- a/tools/krakentools/beta_diversity.xml
+++ b/tools/krakentools/beta_diversity.xml
@@ -52,34 +52,31 @@ beta_diversity.py
 
     </inputs>
     <outputs>
-        <data name="output" format="txt" />
+        <data name="output" format="tabular" />
     </outputs>
     <tests>
         <test>
             <param name="inputs" value="beta_bracken_1.tabular,beta_bracken_2.tabular,beta_bracken_3.tabular"/>
             <param name="type" value="bracken"/>
-            <output name="output" ftype="txt">
-		 <assert_contents>
-		    <has_text text="beta_bracken_1.tabular"/>
-		    <has_text text="beta_bracken_2.tabular"/>
-		    <has_text text="beta_bracken_3.tabular"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_text_matching expression="#[012]&#9;beta_[a-z]+_[123].tabular \([0-9]+ reads\)" n="3"/>
+                    <has_n_columns n="4" comment="#"/>
+                    <has_n_lines n="7"/>
                     <has_text text="0.629"/>
-                    <has_text text="0.993"/>
-                    <has_text text="0.995"/>
                 </assert_contents>
             </output>
         </test>
         <test>
             <param name="inputs" value="beta_kreport_1.tabular,beta_kreport_2.tabular,beta_kreport_3.tabular"/>
             <param name="type" value="kreport"/>
-            <output name="output" ftype="txt">
-		 <assert_contents>
+            <output name="output" ftype="tabular">
+                <assert_contents>
                     <has_text text="beta_kreport_1.tabular"/>
-                    <has_text text="beta_kreport_2.tabular"/>
-                    <has_text text="beta_kreport_3.tabular"/>
+                    <has_text_matching expression="#[012]&#9;beta_[a-z]+_[123].tabular \([0-9]+ reads\)" n="3"/>
+                    <has_n_columns n="4" comment="#"/>
+                    <has_n_lines n="7"/>
                     <has_text text="0.584"/>
-                    <has_text text="0.996"/>
-                    <has_text text="0.995"/>
                 </assert_contents>
             </output>
         </test>
@@ -87,10 +84,11 @@ beta_diversity.py
             <param name="inputs" value="beta_krona_1.tabular,beta_krona_2.tabular"/>
             <param name="type" value="krona"/>
             <param name="level" value="G"/>
-            <output name="output" ftype="txt">
-		<assert_contents>
-		    <has_text text="beta_krona_1.tabular"/>
-		    <has_text text="beta_krona_2.tabular"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_text_matching expression="#[01]&#9;beta_[a-z]+_[12].tabular \([0-9]+ reads\)" n="2"/>
+                    <has_n_columns n="3" comment="#"/>
+                    <has_n_lines n="5"/>
                     <has_text text="0.993"/>
                 </assert_contents>
             </output>