patch krakentools beta_diversity.xml (#6553)

* patch krakentools beta_diversity.xml

* add re.sub to beta_diversity.xml

* patch beta_diversity.xml

* update test unit in beta_diversity.xml

* make output tabular and improve assertions

* fix re.sub in beta diversity

* Update tools/krakentools/beta_diversity.xml

---------

Co-authored-by: mthang <mthang@qfab.org>
Co-authored-by: Matthias Bernt <m.bernt@ufz.de>

Author: 3 people

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>

tools/krakentools/beta_diversity.xml

@@ -7,10 +7,19 @@
     <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
+#import re
+#set input_names=[]
+
+#for $input in $inputs
+        #set identifier = re.sub('[^\s\w\-.]', '_', str($input.element_identifier))
+	#silent $input_names.append($identifier)
+	ln -s '$input' '${identifier}' &&
+#end for
+
 beta_diversity.py 
     --inputs
-    #for $input in $inputs 
-        '$input' 
+    #for $input_name in $input_names
+	'${input_name}' 
     #end for
     --type '$sample.type'
     #if $sample.type == 'kreport'
@@ -43,37 +52,43 @@ 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">
+            <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">
+            <output name="output" ftype="tabular">
                 <assert_contents>
+                    <has_text text="beta_kreport_1.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>
         <test>
             <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>        
+            <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>

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>