# HG changeset patch
# User bebatut
# Date 1446731051 18000
# Node ID 31dd7ace2be45715a7141505d81b72c551448a6d
# Parent 2d1a2051728009dd7979fdadc455d59bca6ec8ca
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 90c51a29d5aaab3f8dea67ac12098dc386e23b4e-dirty
diff -r 2d1a20517280 -r 31dd7ace2be4 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Thu Nov 05 08:44:11 2015 -0500
@@ -0,0 +1,64 @@
+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:
+
+```
+
+```
+
+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
\ No newline at end of file
diff -r 2d1a20517280 -r 31dd7ace2be4 metaphlan2.xml
--- a/metaphlan2.xml Wed Oct 28 12:41:43 2015 -0400
+++ b/metaphlan2.xml Thu Nov 05 08:44:11 2015 -0500
@@ -105,28 +105,28 @@
-
-
-
+
+
+
-
-
- !bowtie2_output
+ bowtie2_output != '--no_map'
-
sam_output
-
biom_output
@@ -136,6 +136,18 @@
+
+
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+