# HG changeset patch
# User bebatut
# Date 1446049440 14400
# Node ID 9f341c9cfa6a9a1c34d2b92a80924023a6187a0b
# Parent  8ce82a6b20d7c49ad13cdf02fcce9be5bf7abc09
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 259ec654231c792a102f99ab7bfd63cbabd4874a-dirty

diff -r 8ce82a6b20d7 -r 9f341c9cfa6a metaphlan2.xml
--- a/metaphlan2.xml	Wed Oct 28 11:48:03 2015 -0400
+++ b/metaphlan2.xml	Wed Oct 28 12:24:00 2015 -0400
@@ -35,21 +35,14 @@
 
             #if $analysis_type.analysis_type_select == "rel_ab"
                 --tax_lev $analysis_type.taxonomic_level 
-            #elif $analysis_type.analysis_type_select == "marker_ab_table"
-                #if $analysis_type.nreads != ''
-                    --nreads $analysis_type.nreads
-                #end if 
-            #elif $analysis_type.analysis_type_select == "marker_pres_table"
-                #if $analysis_type.pres_th != ''
-                    --pres_th $analysis_type.pres_th 
-                #end if
+            #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
 
             --min_cu_len $min_cu_len
-
-            #if $min_alignment_len != ''
-                --min_alignment_len $min_alignment_len
-            #end if
+            --min_alignment_len $min_alignment_len
 
             $ignore_viruses
             $ignore_eukaryotes
@@ -58,10 +51,11 @@
 
             --stat_q $stat_q
 
-            #if $sam_output:
+            #if $sam_output
                 -s $sam_output_file
             #endif
-            #if $biom_output:
+
+            #if $biom_output
                 -biom $biom_output_file
             #endif
 
@@ -169,16 +163,16 @@
 
 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
 
 -----
 
@@ -189,9 +183,9 @@
 
 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>