# HG changeset patch
# User bebatut
# Date 1466071691 14400
# Node ID 8991e05c44e41a07d24ea399eddfb3b3a8f0d057
# Parent  d2448d2bf1f835d5fe02e36a52c79816ad005168
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty

diff -r d2448d2bf1f8 -r 8991e05c44e4 metaphlan2.xml
--- a/metaphlan2.xml	Wed Jun 01 10:45:26 2016 -0400
+++ b/metaphlan2.xml	Thu Jun 16 06:08:11 2016 -0400
@@ -146,7 +146,7 @@
 
     <outputs>
         <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
-        <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: Sam file" />
+        <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />
     </outputs>
 
     <tests>
@@ -171,7 +171,7 @@
     <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/>`_.
+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/>`_.
 
 **Inputs**
 
@@ -199,11 +199,11 @@
         }
   }
 
-The marker names correspond to sequence name in corresponding fasta file with marker gene sequences.
+The marker name correspond to the corresponding sequence name in the FastA file containing marker gene sequences.
 
 **Outputs**
 
-The main output file is a tab-separated output file of the predicted taxon relative abundances.
+The main output file is a tab-separated file with the predicted taxon relative abundances.
 
     ]]></help>
 
diff -r d2448d2bf1f8 -r 8991e05c44e4 metaphlan2_macros.xml
--- a/metaphlan2_macros.xml	Wed Jun 01 10:45:26 2016 -0400
+++ b/metaphlan2_macros.xml	Thu Jun 16 06:08:11 2016 -0400
@@ -3,6 +3,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.2.5">bowtie2</requirement>
+            <requirement type="package" version="1.9">numpy</requirement>
             <requirement type="package" version="2.5.0">metaphlan2</requirement>
         </requirements>
     </xml>
@@ -19,4 +20,4 @@
                    description="" />
         </stdio>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r d2448d2bf1f8 -r 8991e05c44e4 metaphlan2krona.xml
--- a/metaphlan2krona.xml	Wed Jun 01 10:45:26 2016 -0400
+++ b/metaphlan2krona.xml	Thu Jun 16 06:08:11 2016 -0400
@@ -7,7 +7,7 @@
     </macros>
 
     <expand macro="requirements"/>
-    <expand macro="stdio"/>    
+    <expand macro="stdio"/>
 
     <version_command>
 <![CDATA[
@@ -16,7 +16,7 @@
     </version_command>
 
     <command>
-<![CDATA[        
+<![CDATA[
         metaphlan2krona.py
             -p $input_file
             -k $krona
@@ -28,27 +28,27 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Krona file" />
+        <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" />
     </outputs>
 
     <tests>
         <test>
             <param name="input_file" value="community_profile.tabular"/>
             <output name="krona" file="formatted_to_krona.tabular"/>
-        </test>      
+        </test>
     </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/>`_.
+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 format MetaPhlAn2 output for Krona.
+This tool formats MetaPhlAn2 output to be ready for Krona.
 
     ]]></help>
 
     <citations>
         <citation type="doi">10.1038/nmeth.3589</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff -r d2448d2bf1f8 -r 8991e05c44e4 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 01 10:45:26 2016 -0400
+++ b/tool_dependencies.xml	Thu Jun 16 06:08:11 2016 -0400
@@ -1,5 +1,8 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="57b37f63cb84" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
     <package name="bowtie2" version="2.2.5">
         <repository changeset_revision="30bd7eaeddbf" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>