--- a/summarize_taxa.xml	Mon Jul 10 16:41:35 2017 -0400
+++ b/summarize_taxa.xml	Sat Aug 05 07:19:08 2017 -0400
@@ -1,34 +1,34 @@
 <tool id="qiime_summarize_taxa" name="Summarize taxa" version="@WRAPPER_VERSION@.0">
-    <description>and store results in a new table or appended to an existing mapping file</description>
+    <description> and store results in a new table or appended to an existing mapping file (summarize_taxa)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>summarize_taxa.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        summarize_taxa.py
-            -i '$otu_table_fp'
-            -o summarize_taxa
-            -L '$level'
-            #if str($mapping) != 'None':
-                -m '$mapping'
-            #end if
-            --md_identifier $md_identifier
-            $md_as_string
-            $absolute_abundance
-            #if str( $lower_percentage )
-                -l '$lower_percentage'
-            #end if
-            #if str( $upper_percentage)
-                -u '$upper_percentage'
-            #end if
-            $transposed_output
-            $suppress_classic_table_output
-            $suppress_biom_table_output
+summarize_taxa.py
+    -i '$otu_table_fp'
+    -o summarize_taxa
+    -L '$level'
+    #if str($mapping) != 'None':
+        -m '$mapping'
+    #end if
+    --md_identifier $md_identifier
+    $md_as_string
+    $absolute_abundance
+    #if str( $lower_percentage )
+        -l '$lower_percentage'
+    #end if
+    #if str( $upper_percentage)
+        -u '$upper_percentage'
+    #end if
+    $transposed_output
+    $suppress_classic_table_output
+    $suppress_biom_table_output
     ]]></command>
     <inputs>
-        <param argument="--otu_table_fp" type="data" format="tabular,tsv,txt,biom" label="Input OTU table" help="(-i/)"/>
-        <param argument="--level" type="select" label="Taxonomic level to summarize by" multiple="True" display="checkboxes">
+        <param argument="--otu_table_fp" type="data" format="tabular,tsv,txt,biom" label="Input OTU table"/>
+        <param argument="--level" type="select" label="Taxonomic level to summarize by" multiple="true" display="checkboxes">
             <option value="1">Kingdom</option>
             <option value="2" selected="true">Phylum</option>
             <option value="3" selected="true">Class</option>
@@ -37,37 +37,37 @@
             <option value="6" selected="true">Genus</option>
             <option value="7">Species</option>
         </param>
-        <param argument="--mapping" type="data" format="tabular,tsv,csv" label="Input metadata mapping (optional)" help="If supplied, then the taxon information will be added to this file. This option is useful for coloring PCoA plots by taxon abundance or to perform statistical tests of taxon/mapping associations" optional="True"/>
+        <param argument="--mapping" type="data" format="tabular,tsv,csv" label="Input metadata mapping" optional="true" help="If supplied, then the taxon information will be added to this file. This option is useful for coloring PCoA plots by taxon abundance or to perform statistical tests of taxon/mapping associations"/>
         <param argument="--md_identifier" type="text" value="taxonomy" label="Relevant observation metadata key"/>
-        <param argument="--md_as_string" type="boolean" label="Include metadata as string?" truevalue="--md_as_string" falsevalue="" checked="False" help="By default, metadata is included as list"/>
-        <param argument="--absolute_abundance" type="boolean" label="Report absolute abundance?" truevalue="--absolute_abundance" falsevalue="" checked="False" help="By default, relative abundance is reported"/>
-        <param argument="lower_percentage" type="float" label="Percentage threshold to remove highly present OTU (optional)" help="If present, OTUs having higher absolute abundance are trimmed. To remove OTUs that make up more than 5% of the total dataset you would pass 0.05" optional="True"/>
-        <param argument="--upper_percentage" type="float" label="Percentage threshold to remove lowly present OTU (optional)" help="If present, OTUs having lower absolute abundance are trimmed. To remove the OTUs that makes up less than 45% of the total dataset you would pass 0.45" optional="True"/>
-        <param argument="--transposed_output" type="boolean" label="Transpose output?" truevalue="--transposed_output" falsevalue="" checked="False" help="If checked, the output will be written transposed from the regular output. This is helpful in cases when you want to use Site Painter to visualize your data"/>
-        <param argument="--suppress_classic_table_output" type="boolean" label="Suppress creation of the classic (TSV) format taxon table?" truevalue="--suppress_classic_table_output" falsevalue="" checked="False" help="This option is ignored if a mapping file is present"/>
-        <param argument="--suppress_biom_table_output" type="boolean" label="Suppress creation of the BIOM-formatted taxon table?" truevalue="--suppress_biom_table_output" falsevalue="" checked="False" help="This option is ignored if a mapping file is present"/>
+        <param argument="--md_as_string" type="boolean" truevalue="--md_as_string" falsevalue="" checked="false" label="Include metadata as string?" help="By default, metadata is included as list"/>
+        <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="Report absolute abundance?" help="By default, relative abundance is reported"/>
+        <param argument="lower_percentage" type="float" optional="true" label="Percentage threshold to remove highly present OTU" help="If present, OTUs having higher absolute abundance are trimmed. To remove OTUs that make up more than 5% of the total dataset you would pass 0.05"/>
+        <param argument="--upper_percentage" type="float" label="Percentage threshold to remove lowly present OTU" help="If present, OTUs having lower absolute abundance are trimmed. To remove the OTUs that makes up less than 45% of the total dataset you would pass 0.45"/>
+        <param argument="--transposed_output" type="boolean" truevalue="--transposed_output" falsevalue="" checked="false" label="Transpose output?" help="If checked, the output will be written transposed from the regular output. This is helpful in cases when you want to use Site Painter to visualize your data"/>
+        <param argument="--suppress_classic_table_output" type="boolean" truevalue="--suppress_classic_table_output" falsevalue="" checked="false" label="Suppress creation of the classic (TSV) format taxon table?" help="This option is ignored if a mapping file is present"/>
+        <param argument="--suppress_biom_table_output" type="boolean" truevalue="--suppress_biom_table_output" falsevalue="" checked="false" label="Suppress creation of the BIOM-formatted taxon table?" help="This option is ignored if a mapping file is present"/>
     </inputs>
     <outputs>
         <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt" label="${tool.name} on ${on_string}: L1 tab">
-            <filter>"1" in level and suppress_classic_table_output is False</filter>
+            <filter>"1" in level and suppress_classic_table_output is false</filter>
         </data>
         <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt" label="${tool.name} on ${on_string}: L2 tab">
-            <filter>"2" in level and suppress_classic_table_output is False</filter>
+            <filter>"2" in level and suppress_classic_table_output is false</filter>
         </data>
         <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt" label="${tool.name} on ${on_string}: L3 tab">
-            <filter>"3" in level and suppress_classic_table_output is False</filter>
+            <filter>"3" in level and suppress_classic_table_output is false</filter>
         </data>
         <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt" label="${tool.name} on ${on_string}: L4 tab">
-            <filter>"4" in level and suppress_classic_table_output is False</filter>
+            <filter>"4" in level and suppress_classic_table_output is false</filter>
         </data>
         <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt" label="${tool.name} on ${on_string}: L5 tab">
-            <filter>"5" in level and suppress_classic_table_output is False</filter>
+            <filter>"5" in level and suppress_classic_table_output is false</filter>
         </data>
         <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt" label="${tool.name} on ${on_string}: L6 tab">
-            <filter>"6" in level and suppress_classic_table_output is False</filter>
+            <filter>"6" in level and suppress_classic_table_output is false</filter>
         </data>
         <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt" label="${tool.name} on ${on_string}: L7 tab">
-            <filter>"7" in level and suppress_classic_table_output is False</filter>
+            <filter>"7" in level and suppress_classic_table_output is false</filter>
         </data>
     </outputs>
     <tests>