Mercurial > repos > bebatut > graphlan

diff graphlan.xml @ 2:64e69b47b4ec draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit fe1ede437f1b0e414d84d75e6a607047d1678444-dirty
author bebatut
date Mon, 02 May 2016 05:44:20 -0400
parents 5cdaa98d9376
children
line wrap: on
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--- a/graphlan.xml	Fri Apr 01 05:51:57 2016 -0400
+++ b/graphlan.xml	Mon May 02 05:44:20 2016 -0400
@@ -1,14 +1,18 @@
-<tool id="graphlan" name="GraPhlAn" version="1.0">
+<tool id="graphlan" name="GraPhlAn" version="0.9.7">
 
     <description>to produce graphical output of an input tree</description>
 
-    <requirements>
-        <requirement type="package" version="1.66">biopython</requirement>
-        <requirement type="package" version="1.4">matplotlib</requirement>
-        <requirement type="package" version="1.0">graphlan</requirement>
-    </requirements>
+    <macros>
+        <import>graphlan_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
 
     <stdio>
+        <regex match="Warning"
+               source="stderr"
+               level="warning"
+               description="" />
     </stdio>
 
     <version_command>
@@ -49,11 +53,9 @@
     </command>
 
     <inputs>
-        <param name="input_tree" type="data" format="txt" label="Input tree in 
-            PhlyloXML format" help=""/>
+        <param name="input_tree" type="data" format="txt" label="Input tree" help="The tree must be in PhlyloXML, Newick or text format."/>
 
-        <param name='format' type="select" label="Output format"
-            help="(--format)">
+        <param name='format' type="select" label="Output format" help="(--format)">
             <option value="png" selected="true">PNG</option>
             <option value="pdf">PDF</option>
             <option value="ps">PS</option>
@@ -97,23 +99,19 @@
 
     <tests>
         <test>
-            <param name="input_tree" value="output_modified_tree.txt"/>
-            <param name='format' value="png"/>
+            <param name="input_tree" value="intermediary_tree.txt"/>
+            <param name="format" value="png"/>
             <param name="dpi" value="100"/>
             <param name="size" value="7"/>
             <param name="pad" value="2"/>
-            <output name="png_output_image" value="output_image.png" />
+            <output name="png_output_image" file="png_image.png" />
         </test>
     </tests>
 
     <help><![CDATA[
-
 **What it does**
 
-GraPhlAn is a software tool for producing high-quality circular 
-representations of taxonomic and phylogenetic trees. GraPhlAn focuses on 
-concise, integrative, informative, and publication-ready representations of 
-phylogenetically- and taxonomically-driven investigation.
+GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
 
 For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
 
@@ -121,4 +119,4 @@
 
     <citations>
     </citations>
-</tool>
\ No newline at end of file
+</tool>