# HG changeset patch
# User bebatut
# Date 1459417529 14400
# Node ID 3f52f2d65d41ef1a88c4e0061242a2bf9142e5d6
# Parent  e8e0f835b4b6382d840a2393c15ad118a078f2f4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty

diff -r e8e0f835b4b6 -r 3f52f2d65d41 metaphlan2.xml
--- a/metaphlan2.xml	Thu Mar 31 03:25:48 2016 -0400
+++ b/metaphlan2.xml	Thu Mar 31 05:45:29 2016 -0400
@@ -78,10 +78,10 @@
         <conditional name="analysis_type">
             <param name="analysis_type_select" type="select" label="Type of analysis to perform">
               <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
-              <option value="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</option>
               <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
               <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
               <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
+              <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
               <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
             </param>
             <when value="rel_ab">
@@ -96,12 +96,12 @@
                 <option value="s">Species only</option>
               </param>
             </when>
-            <when value="rel_ab_w_read_stats"/>
             <when value="reads_map"/>
             <when value="clade_profiles"/>
             <when value="marker_ab_table">
                 <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/>
             </when>
+            <when value="marker_counts"/>
             <when value="marker_pres_table">
                 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
             </when>
diff -r e8e0f835b4b6 -r 3f52f2d65d41 metaphlan2krona.xml
--- a/metaphlan2krona.xml	Thu Mar 31 03:25:48 2016 -0400
+++ b/metaphlan2krona.xml	Thu Mar 31 05:45:29 2016 -0400
@@ -4,7 +4,7 @@
 
     <requirements>
         <requirement type="package" version="2.2.5">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
+        <requirement type="package" version="2.2.0">metaphlan2</requirement>
     </requirements>
 
     <stdio>