# HG changeset patch
# User bebatut
# Date 1446046665 14400
# Node ID 11bb77fab91f2b409ad107ca3782d7841d2cb34d
# Parent  35d3ad2fb7a4a0eb78387085251939a78d18b9b4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty

diff -r 35d3ad2fb7a4 -r 11bb77fab91f metaphlan2.xml
--- a/metaphlan2.xml	Wed Oct 28 11:14:06 2015 -0400
+++ b/metaphlan2.xml	Wed Oct 28 11:37:45 2015 -0400
@@ -92,16 +92,16 @@
               </param>
             </when>
             <when value="marker_ab_table">
-                <param name="nreads" type="integer" 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"/>
+                <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_pres_table">
-                <param name="pres_th" type="integer" label=" Threshold for calling a marker present" help=""/>
+                <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
             </when>
         </conditional>
 
         <param name="min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances" help=""/>
 
-        <param name="min_alignment_len" type="integer" label="The sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/>
+        <param name="min_alignment_len" type="integer" value="0" label="The sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/>
 
         <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
         <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
@@ -159,14 +159,40 @@
 
 **Input**
 
+Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced
+SAM file or an intermediary mapping file of the metagenome generated by a 
+previous MetaPhlAn
+
 -----
 
 **Parameters**
 
+Several parameters can modulate the MetaPhlAn execution
+
+    - Mapping arguments
+        - Test to avoid saving the output of BowTie2
+    - Post-mapping arguments
+        - Taxonomic level for the relative abundance output
+        - Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
+        - Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
+        - Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
+        - Quantile value
+    - Additional analysis types and arguments
+        - Type of analyse to perform and some parameters for specific analysis type
+
 -----
 
 **Outputs**
 
+The main output file is a tab-separated output file of the predicted taxon 
+relative abundances.
+
+Given the choosen parameters, other output files can be:
+
+    - a sam output file
+    - a biom output fime
+    - a BowTie2 output file
+
     ]]></help>
 
     <citations>