# HG changeset patch
# User bebatut
# Date 1446800658 18000
# Node ID 58e0316371116e4d9e500f970595e697620708da
# Parent  dcd6f25e375b16e34de720f98feb554f9500dce1
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 757604ca54eff007917e5f4c4735b1728988c321-dirty

diff -r dcd6f25e375b -r 58e031637111 metaphlan2.xml
--- a/metaphlan2.xml	Thu Nov 05 10:54:40 2015 -0500
+++ b/metaphlan2.xml	Fri Nov 06 04:04:18 2015 -0500
@@ -35,11 +35,7 @@
             --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl 
             --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
 
-            #if $bowtie2_output:
-                --bowtie2out $bowtie2_output_file
-            #else
-                --no_map
-            #end if
+            --no_map
 
             -t $analysis_type.analysis_type_select
             #if $analysis_type.analysis_type_select == "rel_ab"
@@ -113,7 +109,6 @@
 
         <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
 
-        <param name="bowtie2_output" type='boolean' checked="true" label="Store the output of BowTie2?" help="" />
         <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
         <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
     </inputs>
@@ -123,12 +118,6 @@
             metadata="input_sequence_file" 
             label="Profile of communities on ${on_string} (MetaPhlAn)" />
 
-        <data format="bowtie2" name="bowtie2_output_file" 
-            metadata="input_sequence_file" 
-            label="Bowtie2 output on ${on_string} (MetaPhlAn)">
-            <filter>bowtie2_output</filter>
-        </data>
-
         <data format="sam" name="sam_output_file" 
             metadata="input_sequence_file" 
             label="Sam output on ${on_string} (MetaPhlAn)">
@@ -153,10 +142,10 @@
             <param name="ignore_bacteria" value="" />
             <param name="ignore_archaea" value="" />
             <param name="stat_q" value="0.1" />
-            <param name="bowtie2_output" value='True' />
             <param name="sam_output" value='False' />
-            <param name="biom_output" value='False' />
+            <param name="biom_output" value='True' />
             <output name="output_file" file="profiled_metagenome.txt"/>
+            <output name="biom_output_file" file="biom.biom"/>
         </test>
     </tests>
 
@@ -166,9 +155,8 @@
 
 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
-
-.. _MetaPhlAn2 user manual: https://bitbucket.org/biobakery/metaphlan2
+sequencing data with species level resolution. For more information, check the 
+`user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
 
 -----
 
diff -r dcd6f25e375b -r 58e031637111 test-data/biom.biom
diff -r dcd6f25e375b -r 58e031637111 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 05 10:54:40 2015 -0500
+++ b/tool_dependencies.xml	Fri Nov 06 04:04:18 2015 -0500
@@ -7,12 +7,13 @@
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://bitbucket.org/biobakery/metaphlan2/get/default.zip</action>
+                <action type="make_directory">$INSTALL_DIR/metaphlan2</action>
                 <action type="move_directory_files">
                     <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
+                    <destination_directory>$INSTALL_DIR/metaphlan2</destination_directory>
                 </action>
                 <action type="set_environment">
-                    <environment_variable action="set_to" name="METAPHLAN2_DIR">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="METAPHLAN2_DIR">$INSTALL_DIR/biobakery-metaphlan2-d1016b2f4e10/</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>