diff graphlan.xml @ 0:83baf73b0e79 draft default tip

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/graphlan.xml	Thu May 26 09:38:11 2016 -0400
@@ -0,0 +1,122 @@
+<tool id="graphlan" name="GraPhlAn" version="0.9.7">
+
+    <description>to produce graphical output of an input tree</description>
+
+    <macros>
+        <import>graphlan_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+
+    <stdio>
+        <regex match="Warning"
+               source="stderr"
+               level="warning"
+               description="" />
+    </stdio>
+
+    <version_command>
+<![CDATA[
+graphlan.py -v
+]]>
+    </version_command>
+
+    <command>
+<![CDATA[        
+        graphlan.py
+            --format $format
+
+            #if $dpi
+                --dpi $dpi
+            #end if
+
+            --size $size
+
+            #if $pad
+                --pad $pad
+            #end if
+
+            $input_tree
+
+            #if str($format) == "png"
+                $png_output_image
+            #else if str($format) == "pdf"
+                $pdf_output_image
+            #else if str($format) == "ps"
+                $ps_output_image
+            #else if str($format) == "eps"
+                $eps_output_image
+            #else
+                $svg_output_image
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <param name="input_tree" type="data" format="txt" label="Input tree" help="The tree must be in PhlyloXML, Newick or text format."/>
+
+        <param name='format' type="select" label="Output format" help="(--format)">
+            <option value="png" selected="true">PNG</option>
+            <option value="pdf">PDF</option>
+            <option value="ps">PS</option>
+            <option value="eps">EPS</option>
+            <option value="svg">SVG</option>
+        </param>
+
+        <param name="dpi" type="integer" label="Dpi of the output image
+            (Optional)" help="For non vectorial formats (--dpi)" optional="True"/>
+
+        <param name="size" type="integer" value="7" label="Size of the output image
+            (in inches)" help="(--size)"/>
+
+        <param name="pad" type="integer" label="Distance between the most external 
+            graphical element and the border of the image (Optional)" 
+            help="(--pad)" optional="True"/>
+    </inputs>
+
+    <outputs>
+        <data format="png" name="png_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="png"</filter>
+        </data>
+        <data format="pdf" name="pdf_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="pdf"</filter>
+        </data>
+        <data format="ps" name="ps_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="ps"</filter>
+        </data>
+        <data format="eps" name="eps_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="eps"</filter>
+        </data>
+        <data format="svg" name="svg_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="svg"</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <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" 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.
+
+For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>