# HG changeset patch
# User bebatut
# Date 1454400831 18000
# Node ID 1479a794253d99c8a96f29b9e455224e5f075944
# Parent  8b151cff43e0a62f9701ca44a2f309530118e756
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit d28e31b1b4dbcc3c406a4e8a5a41ac4576bf4f43-dirty

diff -r 8b151cff43e0 -r 1479a794253d metaphlan2krona.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan2krona.xml	Tue Feb 02 03:13:51 2016 -0500
@@ -0,0 +1,65 @@
+<tool id="metaphlan2krona" name="Format MetaPhlAn2" version="0.1.0">
+
+    <description>output for Krona</description>
+
+    <requirements>
+        <requirement type="package" version="2.2.5">bowtie2</requirement>
+        <requirement type="package" version="2.0">metaphlan2</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" level="fatal"   description="" />
+        <regex match="ERROR"
+               source="stderr"
+               level="fatal"
+               description="" />
+        <regex match="WARNING"
+               source="stderr"
+               level="warning"
+               description="" />
+    </stdio>
+
+    <version_command>
+<![CDATA[
+python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py -v
+]]>
+    </version_command>
+
+    <command>
+<![CDATA[        
+        python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py
+            -p $input_file
+            -k $krona
+]]>
+    </command>
+
+    <inputs>
+        <param name="input_file" type="data" format="tabular,txt" label="Input 
+            file (MetaPhlAN2 output)" help="(--profile)"/>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="krona" 
+            label="${tool.name} on ${on_string}: Krona file" />
+    </outputs>
+
+    <tests>      
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+MetaPhlAn is a computational tool for profiling the composition of microbial 
+communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun 
+sequencing data with species level resolution. For more information, check the 
+`user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
+
+This tool format MetaPhlAn2 output for Krona.
+
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1038/nmeth.3589</citation>
+    </citations>
+</tool>
\ No newline at end of file