diff taxonomy_krona_chart.xml @ 10:e9005d1f3cfd draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 46ae76d42d29ce02cf05b6ab735e0c305a86f9cd"

--- a/taxonomy_krona_chart.xml	Sat Nov 30 13:05:03 2019 -0500
+++ b/taxonomy_krona_chart.xml	Fri Dec 18 16:16:12 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.7.1">
+<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.7.1+galaxy0">
   <description>from taxonomic profile</description>
   <requirements>
     <requirement type="package" version="2.7.1">krona</requirement>
@@ -10,22 +10,17 @@
     #if $type_of_data.input[0].is_of_type('taxonomy'):
         ktImportGalaxy
         -d '${type_of_data.max_rank}'
-        -n '${root_name}'
-        -o '${output}'
-        ${combine_inputs}
-        #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
-            '${input_dataset},${input_count}'
-        #end for
     #else:
         ktImportText
-        -n '${root_name}'
-        -o '${output}'
-        ${combine_inputs}
-        #for $input_dataset in $type_of_data.input:
-             #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
-            '${input_dataset},${identifier}'
-        #end for
     #end if
+
+    -n '${root_name}'
+    -o '${output}'
+    ${combine_inputs}
+    #for $input_dataset in $type_of_data.input:
+        #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
+        '${input_dataset},${identifier}'
+    #end for
     &&
     if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi
   ]]></command>
@@ -79,7 +74,30 @@
       <param name="max_rank" value="Genus"/>
       <param name="root_name" value="Root"/>
       <param name="combine_inputs" value="False"/>
-      <output name="output" file="krona_test1.html" ftype="html" lines_diff="102"/>
+      <output name="output" ftype="html">
+        <assert_contents>
+          <has_text text="KRONA"/>
+          <has_text text="taxonomy_data"/>
+          <has_text text="Eukaryota"/>
+          <has_text text="Chordata"/>
+          <has_text text="Rodentia"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="type_of_data_selector" value="taxonomy"/>
+      <param name="input" value="taxonomy_data.tax,tax2.tax" ftype="taxonomy" />
+      <param name="max_rank" value="Genus"/>
+      <param name="root_name" value="Root"/>
+      <param name="combine_inputs" value="False"/>
+      <output name="output" ftype="html">
+        <assert_contents>
+          <has_text text="KRONA"/>
+          <has_text text="taxonomy_data"/>
+          <has_text text="tax2"/>
+          <has_text text="Proteobacteria"/>
+        </assert_contents>
+      </output>
     </test>
     <test><!-- test with tabular inputs and multiple datasets -->
       <param name="type_of_data_selector" value="text"/>