diff README.md @ 9:31dd7ace2be4 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 90c51a29d5aaab3f8dea67ac12098dc386e23b4e-dirty

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+Galaxy wrapper for MetaPhlAn2
+=============================
+
+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)
+
+# Installation
+
+## Automated installation
+
+On a Galaxy instance, the wrapper can be automatically installed using the 
+ToolShed. This will automatically install the dependencies, configure the Galaxy
+instance for the tool and data, ...
+
+## Manual installation
+
+For manual installation, the files `metaphlan2.xml` must be put in the `tools/metaphlan2/`
+ folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as 
+normal:
+
+```
+<section name="Profile microbial community composition" id="metaphlan2">
+    <tool file="metaphlan2/metaphlan2.xml" />
+</section>
+```
+
+MetaPhlAn2 must be installed somewhere on the system path. It can be done using:
+
+```
+planemo dependency_script ~/repositories/galaxytools/tools/metaphlan2/
+bash dep_install.sh
+source env.sh
+```
+
+To test the Galaxy integration, the functional tests can be runned:
+
+```
+./run_tests.sh -sid metaphlan2
+```
+
+# Bug Reports
+
+Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues).
+
+# Developers
+
+A release can be pushed to the test or main "Galaxy Tool Shed", using the following 
+Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`):
+
+```
+planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/metaphlan2/
+```
+
+or:
+
+```
+planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/metaphlan2/
+```
+
+# License (Apache 2) 
+
+This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details
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