diff kraken-report.xml @ 4:a3a7440fc618 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_report/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd

--- a/kraken-report.xml	Wed Mar 23 11:01:19 2016 -0400
+++ b/kraken-report.xml	Mon Aug 07 17:29:32 2017 -0400
@@ -1,22 +1,22 @@
-<tool id="kraken-report" name="Kraken-report" version="1.2.1">
-    <description>
-        view a sample report of your classification
-    </description>
-    
+<tool id="kraken-report" name="Kraken-report" version="@WRAPPER_VERSION@">
+    <description>view sample report of a classification</description>
+
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-        <![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
         @SET_DATABASE_PATH@ &&
-        kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
-        ]]>
-    </command>
+
+        kraken-report
+            @INPUT_DATABASE@
+            '${kraken_output}'
+            > '$output_report'
+    ]]></command>
     <inputs>
-        <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/>
+        <param name="kraken_output" type="data" format="tabular" label="Kraken output" help="Select taxonomy classification produced by kraken"/>
+
         <expand macro="input_database" />
     </inputs>
     <outputs>
@@ -26,12 +26,11 @@
         <test>
             <param name="kraken_output" value="kraken_report_test1.tab" ftype="tabular"/>
             <param name="kraken_database" value="test_db"/>
-            <output name="output_report" file="kraken_report_test1_output.tab" ftype="tabular"/>
+            <output name="output_report" ftype="tabular" file="kraken_report_test1_output.tab"/>
         </test>
     </tests>
 
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 .. class:: warningmark
 
@@ -52,7 +51,6 @@
 
 The scientific names are indented using spaces, according to the tree
 structure specified by the taxonomy.
-    ]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>