Mercurial > repos > iuc > metaphlan2krona

diff metaphlan2krona.xml @ 0:fdbd63e92b01 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
author: iuc
date: Sat, 04 Mar 2017 12:24:03 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan2krona.xml	Sat Mar 04 12:24:03 2017 -0500
@@ -0,0 +1,48 @@
+<tool id="metaphlan2krona" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0">
+
+    <description>output for Krona</description>
+
+    <macros>
+        <import>metaphlan2_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <version_command>metaphlan2krona.py -v</version_command>
+
+    <command>
+<![CDATA[
+        metaphlan2krona.py
+            --profile '$profile'
+            -k '$krona'
+]]>
+    </command>
+
+    <inputs>
+        <param argument="--profile" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)"/>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="profile" value="community_profile.tabular"/>
+            <output name="krona" file="formatted_to_krona.tabular"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+MetaPhlAn is a computational tool to profile the structure and 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 formats MetaPhlAn2 output to be ready for Krona.
+
+    ]]></help>
+
+    <expand macro="citations"/>
+</tool>