changeset 4:8e2be617b437 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit d62a0a2d4d0a8ac23014f09c1958d7ca0ea4fbb6

--- a/taxonomy_krona_chart.xml	Tue Mar 29 08:53:26 2016 -0400
+++ b/taxonomy_krona_chart.xml	Thu May 04 06:04:23 2017 -0400
@@ -1,39 +1,30 @@
-<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.0">
+<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1">
   <description>from taxonomic profile</description>
   <requirements>
-    <requirement type="package" version="2.6">krona</requirement>
+    <requirement type="package" version="2.6.1">krona</requirement>
   </requirements>
   <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
-  <command>
-  <![CDATA[
-
-  #if $type_of_data.input[0].is_of_type('taxonomy'):
-
+  <command><![CDATA[
+    #if $type_of_data.input[0].is_of_type('taxonomy'):
         ktImportGalaxy
-        -d "${type_of_data.max_rank}"
-        -n "${root_name}"
-        -o "${output}"
+        -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},${input_count}"
+            '${input_dataset},${input_count}'
         #end for
-
-  #else:
-
+    #else:
         ktImportText
-        -n "${root_name}"
-        -o "${output}"
+        -n '${root_name}'
+        -o '${output}'
         ${combine_inputs}
         #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
-            "${input_dataset},${input_count}"
+            '${input_dataset},${input_count}'
         #end for
-
-  #end if
-
-&& [ -d "${output}.files" ] && ( mkdir "${output.extra_files_path}" && mv "${output}.files" "${output.extra_files_path}/" )
-  ]]>
-
-  </command>
+    #end if
+    && [ -d '${output}.files' ] && ( mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}/' )
+  ]]></command>
   <inputs>
     <conditional name="type_of_data">
       <param name="type_of_data_selector" type="select" label="What is the type of your input data" help="Select between Galaxy Taxonomy and MetaPhlAn Text">
@@ -43,7 +34,7 @@
       <when value="taxonomy">
         <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" />
         <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point">
-            <option value="8">Class</option> 
+            <option value="8">Class</option>
             <option value="0">Show entire tree</option>
             <option value="1">Superkingdom</option>
             <option value="2">Kingdom</option>
@@ -72,7 +63,7 @@
       </when>
     </conditional>
     <param name="root_name" type="text" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/>
-    <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/>
+    <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" checked="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/>
   </inputs>
   <outputs>
     <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
@@ -90,7 +81,7 @@
   <help>
 **What it does**
 
-This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. 
+This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_.
 
 
 .. _Krona: https://github.com/marbl/Krona/wiki
@@ -100,7 +91,7 @@
 **Krona options**
 
 The Galaxy version supports the following options::
-                                                                                                                                                                                      
+
   -n   Name of the highest level.
   -c   Combine data from each file, rather than creating separate datasets within the chart.
   -d   Maximum depth of wedges to include in the chart.
@@ -112,13 +103,11 @@
 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
-.. _MIT license: http://opensource.org/licenses/MIT
+.. _MIT license: https://opensource.org/licenses/MIT
 
 You can use this tool only if you agree to the license terms of: `Krona`_.
 
-.. _Krona: http://sourceforge.net/p/krona/home/krona/
-
-
+.. _Krona: https://github.com/marbl/Krona/wiki
   </help>
   <citations>
         <citation type="doi">10.1186/1471-2105-12-385</citation>

--- a/tool_dependencies.xml	Tue Mar 29 08:53:26 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="krona" version="2.6">
-    <repository changeset_revision="33c81f965131" name="package_krona_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-</tool_dependency>