# HG changeset patch
# User bebatut
# Date 1446050233 14400
# Node ID 9603321a851925f14c215d95a839c45826229f54
# Parent  167876cbcdd558d458c9c2de749b1bed4c9e52d3
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 259ec654231c792a102f99ab7bfd63cbabd4874a-dirty

diff -r 167876cbcdd5 -r 9603321a8519 metaphlan2.xml
--- a/metaphlan2.xml	Wed Oct 28 12:34:12 2015 -0400
+++ b/metaphlan2.xml	Wed Oct 28 12:37:13 2015 -0400
@@ -17,7 +17,8 @@
 ]]>
     </version_command>
 
-    <command><![CDATA[
+    <command>
+<![CDATA[
         python \${METAPHLAN2_DIR}/metaphlan.py
             $input_file
             -o $output_file
@@ -35,14 +36,10 @@
 
             #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 
-                    #end if
-                #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
@@ -57,13 +54,13 @@
 
             #if $sam_output
                 -s $sam_output_file
-            #endif
+            #end if
 
             #if $biom_output
                 -biom $biom_output_file
-            #endif
-
-    ]]></command>
+            #end if
+]]>
+    </command>
 
     <inputs>
         <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
@@ -167,21 +164,21 @@
 
 Several parameters can modulate the MetaPhlAn execution
 
-* Mapping arguments
+    * Mapping arguments
 
-    * Test to avoid saving the output of BowTie2
+        * Test to avoid saving the output of BowTie2
 
-* Post-mapping arguments
+    * 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
+        * 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
+    * Additional analysis types and arguments
 
-    * Type of analyse to perform and some parameters for specific analysis type
+        * Type of analyse to perform and some parameters for specific analysis type
 
 -----
 
@@ -192,9 +189,9 @@
 
 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>