# HG changeset patch
# User bebatut
# Date 1446050052 14400
# Node ID 167876cbcdd558d458c9c2de749b1bed4c9e52d3
# Parent  575f1f4420eee1dbbf56730ecc2111901bb7bc18
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 259ec654231c792a102f99ab7bfd63cbabd4874a-dirty

diff -r 575f1f4420ee -r 167876cbcdd5 metaphlan2.xml
--- a/metaphlan2.xml	Wed Oct 28 12:29:53 2015 -0400
+++ b/metaphlan2.xml	Wed Oct 28 12:34:12 2015 -0400
@@ -35,10 +35,14 @@
 
             #if $analysis_type.analysis_type_select == "rel_ab"
                 --tax_lev $analysis_type.taxonomic_level 
-            #else if $analysis_type.analysis_type_select == "marker_ab_table"
-                --nreads $analysis_type.nreads
-            #else if $analysis_type.analysis_type_select == "marker_pres_table"
-                --pres_th $analysis_type.pres_th 
+            #else
+                #if $analysis_type.analysis_type_select == "marker_ab_table"
+                    --nreads $analysis_type.nreads
+                #else
+                    #if $analysis_type.analysis_type_select == "marker_pres_table"
+                        --pres_th $analysis_type.pres_th 
+                    #end if
+                #end if
             #end if
 
             --min_cu_len $min_cu_len
@@ -163,16 +167,21 @@
 
 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
+* 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
 
 -----
 
@@ -183,9 +192,9 @@
 
 Given the choosen parameters, other output files can be:
 
-- a sam output file
-- a biom output fime
-- a BowTie2 output file
+* a sam output file
+* a biom output fime
+* a BowTie2 output file
 
     ]]></help>