Mercurial > repos > bebatut > metaphlan2

diff metaphlan2krona.xml @ 31:83f06bee818c draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
author bebatut
date Tue, 21 Feb 2017 12:29:37 -0500
parents 99fe591b59fb
children
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--- a/metaphlan2krona.xml	Thu Jun 16 06:07:23 2016 -0400
+++ b/metaphlan2krona.xml	Tue Feb 21 12:29:37 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="metaphlan2krona" name="Format MetaPhlAn2" version="2.5.0">
+<tool id="metaphlan2krona" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0">
 
     <description>output for Krona</description>
 
@@ -9,22 +9,18 @@
     <expand macro="requirements"/>
     <expand macro="stdio"/>
 
-    <version_command>
-<![CDATA[
-metaphlan2krona.py -v
-]]>
-    </version_command>
+    <version_command>metaphlan2krona.py -v</version_command>
 
     <command>
 <![CDATA[
         metaphlan2krona.py
-            -p $input_file
-            -k $krona
+            --profile '$profile'
+            -k '$krona'
 ]]>
     </command>
 
     <inputs>
-        <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/>
+        <param argument="--profile" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)"/>
     </inputs>
 
     <outputs>
@@ -33,7 +29,7 @@
 
     <tests>
         <test>
-            <param name="input_file" value="community_profile.tabular"/>
+            <param name="profile" value="community_profile.tabular"/>
             <output name="krona" file="formatted_to_krona.tabular"/>
         </test>
     </tests>
@@ -48,7 +44,5 @@
 
     ]]></help>
 
-    <citations>
-        <citation type="doi">10.1038/nmeth.3589</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>