# HG changeset patch
# User bebatut
# Date 1459409148 14400
# Node ID e8e0f835b4b6382d840a2393c15ad118a078f2f4
# Parent  51e7d53fcefb463d271ac18954fdc89f3acb6004
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty

diff -r 51e7d53fcefb -r e8e0f835b4b6 README.md
--- a/README.md	Wed Dec 09 11:48:33 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-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
\ No newline at end of file
diff -r 51e7d53fcefb -r e8e0f835b4b6 metaphlan2.xml
--- a/metaphlan2.xml	Wed Dec 09 11:48:33 2015 -0500
+++ b/metaphlan2.xml	Thu Mar 31 03:25:48 2016 -0400
@@ -1,10 +1,10 @@
-<tool id="metaphlan2" name="MetaPhlAn2" version="0.1.0">
+<tool id="metaphlan2" name="MetaPhlAn2" version="2.2.0">
 
     <description>to profile the composition of microbial communities</description>
 
     <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
+        <requirement type="package" version="2.2.5">bowtie2</requirement>
+        <requirement type="package" version="2.2.0">metaphlan2</requirement>
     </requirements>
 
     <stdio>
@@ -26,13 +26,19 @@
     </version_command>
 
     <command>
-<![CDATA[
+<![CDATA[        
+        (which bowtie2 || exit 200)
+
+        &&
+
         python \${METAPHLAN2_DIR}/metaphlan2.py
             $input_file
             -o $output_file
 
             --input_type ${input_file.datatype.file_ext}
             --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl 
+
+            --bowtie2_exe `which bowtie2`
             --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
 
             --no_map
@@ -117,7 +123,7 @@
     </inputs>
 
     <outputs>
-        <data format="txt" name="output_file" 
+        <data format="tabular" name="output_file" 
             metadata="input_sequence_file" 
             label="Profile of communities on ${on_string} (MetaPhlAn)" />
 
@@ -145,8 +151,8 @@
             <param name="ignore_bacteria" value="" />
             <param name="ignore_archaea" value="" />
             <param name="stat_q" value="0.1" />
-            <param name="sam_output" value='False' />
-            <param name="biom_output" value='True' />
+            <param name="sam_output" value='false' />
+            <param name="biom_output" value='true' />
             <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/>
             <output name="biom_output_file" file="metaphlan2_biom.biom"/>
         </test>
diff -r 51e7d53fcefb -r e8e0f835b4b6 metaphlan2krona.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan2krona.xml	Thu Mar 31 03:25:48 2016 -0400
@@ -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
diff -r 51e7d53fcefb -r e8e0f835b4b6 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 09 11:48:33 2015 -0500
+++ b/tool_dependencies.xml	Thu Mar 31 03:25:48 2016 -0400
@@ -3,7 +3,7 @@
     <package name="bowtie2" version="2.2.5">
         <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="metaphlan2" version="2.0">
-        <repository changeset_revision="906e1ca45fe2" name="package_metaphlan_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="metaphlan2" version="2.2.0">
+        <repository changeset_revision="bbac0ef27bb2" name="package_metaphlan2_2_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>