--- a/alpha_rarefaction.xml	Mon Jul 10 16:34:48 2017 -0400
+++ b/alpha_rarefaction.xml	Fri Aug 04 18:26:53 2017 -0400
@@ -1,47 +1,47 @@
 <tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="@WRAPPER_VERSION@.0">
-    <description>A workflow script for performing alpha rarefaction</description>
+    <description>(alpha_rarefaction)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>alpha_rarefaction.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        ## set matplotlib backend
-        echo "backend:agg" > matplotlibrc &&
-        
-        alpha_rarefaction.py
-            --otu_table_fp '$otu_table_fp'
-            --mapping_fp '$mapping_fp'
-            -o alpha_rarefaction
-            #if $parameter_fp
-                --parameter_fp '$parameter_fp'
-            #end if
-            --num_steps '$num_steps'
-            $parallel
-            -O "\${GALAXY_SLOTS:-4}"
-            #if $tree_fp
-                --tree_fp '$tree_fp'
-            #end if
-            --min_rare_depth '$min_rare_depth'
-            #if $max_rare_depth
-                --max_rare_depth '$max_rare_depth'
-            #end if
-            $retain_intermediate_files
+## set matplotlib backend
+echo "backend:agg" > matplotlibrc &&
 
-            && mkdir -p $alpha_rarefaction_plots.files_path
-            && cp alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots
-            && cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path
+alpha_rarefaction.py
+    --otu_table_fp '$otu_table_fp'
+    --mapping_fp '$mapping_fp'
+    -o alpha_rarefaction
+    #if $parameter_fp
+        --parameter_fp '$parameter_fp'
+    #end if
+    --num_steps '$num_steps'
+    $parallel
+    -O "\${GALAXY_SLOTS:-4}"
+    #if $tree_fp
+        --tree_fp '$tree_fp'
+    #end if
+    --min_rare_depth '$min_rare_depth'
+    #if $max_rare_depth
+        --max_rare_depth '$max_rare_depth'
+    #end if
+    $retain_intermediate_files
+
+&& mkdir -p $alpha_rarefaction_plots.files_path
+&& cp alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots
+&& cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path
     ]]></command>
     <inputs>
         <param argument="--otu_table_fp" type="data" format="tabular,txt,tsv,biom" label="OTU table"/>
         <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file"/>
         <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/>
         <param argument="--num_steps" type="integer" value="10" label="Number of steps (or rarefied OTU table sizes) to make between min and max counts"/>
-        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/>
-        <param argument="--tree_fp" type="data" format="tabular,txt,tsv" optional="True" label="Tree file (optional)" help="Required for phylogenetic measures"/>
+        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
+        <param argument="--tree_fp" type="data" format="tabular,txt,tsv" optional="true" label="Tree file (optional)" help="Required for phylogenetic measures"/>
         <param argument="--min_rare_depth" type="integer" value="10" label="Lower limit of rarefaction depths"/>
         <param argument="--max_rare_depth" type="integer" label="Upper limit of rarefaction depths" help="By default, median sequence/sample count is used" optional="True"/>
-        <param argument="--retain_intermediate_files" type="boolean" truevalue="--retain_intermediate_files" falsevalue="" checked="True" label="Retain intermediate files?"/>
+        <param argument="--retain_intermediate_files" type="boolean" truevalue="--retain_intermediate_files" falsevalue="" checked="true" label="Retain intermediate files?"/>
     </inputs>
     <outputs>
         <data name="alpha_rarefaction_plots" format="html" label="${tool.name} on ${on_string}: Alpha rarefaction plots"/>