diff taxonomy_krona_chart.xml @ 2:50f204c82159 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 70d4a2d1563e834d8394dce8017a1f0b7ad74f23

--- a/taxonomy_krona_chart.xml	Mon Aug 17 11:36:09 2015 -0400
+++ b/taxonomy_krona_chart.xml	Wed Mar 02 04:49:06 2016 -0500
@@ -1,7 +1,7 @@
-<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.0.0">
+<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.0">
   <description>from taxonomic profile</description>
   <requirements>
-    <requirement type="package" version="2.5">krona</requirement>
+    <requirement type="package" version="2.6">krona</requirement>
   </requirements>
   <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
   <command>
@@ -10,10 +10,9 @@
   #if $type_of_data.input[0].is_of_type('taxonomy'):
 
         ktImportGalaxy
-        -a
         -d "${type_of_data.max_rank}"
         -n "${root_name}"
-        -o ${output}
+        -o "${output}"
         ${combine_inputs}
         #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
             "${input_dataset},${input_count}"
@@ -22,9 +21,8 @@
   #else:
 
         ktImportText
-        -a
         -n "${root_name}"
-        -o ${output}
+        -o "${output}"
         ${combine_inputs}
         #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
             "${input_dataset},${input_count}"
@@ -32,6 +30,7 @@
 
   #end if
 
+&& [ -d "${output}.files" ] && ( mkdir "${output.extra_files_path}" && mv "${output}.files" "${output.extra_files_path}/" )
   ]]>
 
   </command>
@@ -72,7 +71,7 @@
         <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" />
       </when>
     </conditional>
-    <param name="root_name" type="text" size="20" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/>
+    <param name="root_name" type="text" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/>
     <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/>
   </inputs>
   <outputs>
@@ -94,7 +93,7 @@
 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. 
 
 
-.. _Krona: http://sourceforge.net/p/krona/home/krona/
+.. _Krona: https://github.com/marbl/Krona/wiki
 
 ------