# 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 @@ + + + + + + + + + + + +