# HG changeset patch
# User bebatut
# Date 1446737519 18000
# Node ID bee6cb51b96d6e29d0dcaa365808e1b700982641
# Parent  84dd21255542b9a67c2a14121cfa0c4555235b3f
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit bf4b8a62e4414d68a917f5b72f3aedf34facaff2-dirty

diff -r 84dd21255542 -r bee6cb51b96d metaphlan2.xml
--- a/metaphlan2.xml	Thu Nov 05 10:22:17 2015 -0500
+++ b/metaphlan2.xml	Thu Nov 05 10:31:59 2015 -0500
@@ -35,9 +35,10 @@
             --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl 
             --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
 
-            $bowtie2_output
-            #if not $bowtie2_output
+            # if $bowtie2_output:
                 --bowtie2out $bowtie2_output_file
+            # else:
+                --no_map
             #end if
 
             -t $analysis_type.analysis_type_select
@@ -112,7 +113,7 @@
 
         <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
 
-        <param name="bowtie2_output" type='boolean' checked="true" truevalue="" falsevalue='--no_map' label="Store the output of BowTie2?" help="" />
+        <param name="bowtie2_output" type='boolean' checked="true" label="Store the output of BowTie2?" help="" />
         <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
         <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
     </inputs>
@@ -125,7 +126,7 @@
         <data format="bowtie2" name="bowtie2_output_file" 
             metadata="input_sequence_file" 
             label="Bowtie2 output on ${on_string} (MetaPhlAn)">
-            <filter>bowtie2_output != '--no_map' </filter>
+            <filter>bowtie2_output</filter>
         </data>
 
         <data format="sam" name="sam_output_file" 
@@ -152,7 +153,7 @@
             <param name="ignore_bacteria" value="" />
             <param name="ignore_archaea" value="" />
             <param name="stat_q" value="0.1" />
-            <param name="bowtie2_output" value='--no_map' />
+            <param name="bowtie2_output" value='True' />
             <param name="sam_output" value='False' />
             <param name="biom_output" value='False' />
             <output name="output_file" file="profiled_metagenome.txt"/>