--- a/validate_mapping_file.xml	Mon Jul 10 16:28:25 2017 -0400
+++ b/validate_mapping_file.xml	Fri Aug 04 18:24:23 2017 -0400
@@ -1,39 +1,39 @@
-<tool id="qiime_validate_mapping_file" name="Validate mapping file" version="@WRAPPER_VERSION@.0">
-    <description>to check for required data and format</description>
+<tool id="qiime_validate_mapping_file" name="Check user's metadata mapping file" version="@WRAPPER_VERSION@.0">
+    <description> for required data, valid format (validate_mapping_file)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>validate_mapping_file.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        validate_mapping_file.py
-            --mapping_fp '$mapping_fp'
-            -o validate_mapping_file_output
-            $verbose
-            --char_replace '$char_replace'
-            $not_barcoded
-            $variable_len_barcodes
-            $disable_primer_check
-            #if str($added_demultiplex_field):
-                --added_demultiplex_field '$added_demultiplex_field'
-            #end if
-            $suppress_html
+validate_mapping_file.py
+    --mapping_fp '$mapping_fp'
+    -o validate_mapping_file_output
+    $verbose
+    --char_replace '$char_replace'
+    $not_barcoded
+    $variable_len_barcodes
+    $disable_primer_check
+    #if str($added_demultiplex_field):
+        --added_demultiplex_field '$added_demultiplex_field'
+    #end if
+    $suppress_html
 
-            #if not $suppress_html:
-                && mkdir -p '$html_report.files_path'
-                && mv validate_mapping_file_output/*.html '$html_report'
-                && cp validate_mapping_file_output/overlib.js '$html_report.files_path'
-            #end if
+    #if not $suppress_html:
+        && mkdir -p '$html_report.files_path'
+        && mv validate_mapping_file_output/*.html '$html_report'
+        && cp validate_mapping_file_output/overlib.js '$html_report.files_path'
+    #end if
     ]]></command>
     <inputs>
-       <param argument="--mapping_fp" label="Metadata mapping filepath" type="data" format="tabular,csv,txt" help=""/>
-        <param argument="--verbose" type="boolean" label="Enable printing information to standard out?" truevalue="-v" falsevalue="" checked="False"/>
+       <param argument="--mapping_fp" label="Metadata mapping filepath" type="data" format="tabular,csv,txt"/>
+        <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Enable printing information to standard out?"/>
         <param argument="--char_replace" type="text" value="_" label="Default character used to replace invalid characters found in the mapping file" help="Must be a valid character (alphanumeric, period, or underscore)"/>
-        <param argument="--not_barcoded" type="boolean" label="Are barcodes present?" truevalue="" falsevalue="--not_barcoded" checked="True" help="BarcodeSequence header is still required in mapping file"/>
-        <param argument="--variable_len_barcodes" type="boolean" label="Are barcodes with variable length?" truevalue="" falsevalue="--variable_len_barcodes" checked="True" help=""/>
-        <param argument="--disable_primer_check" type="boolean" label="Disable checks for primers?" truevalue="-disable_primer_check" falsevalue="" checked="False" help="LinkerPrimerSequence header is still required in mapping file"/>
-        <param argument="--added_demultiplex_field" type="text" label="Field to use in the mapping file as additional demultiplexing (optional)" help="It can be used with or without barcodes.  All combinations of barcodes/primers and these fields must be unique. The fields must contain values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'. In this case, 'plate' would be the column header and 'R_2008_12_09' would be the field data (minus quotes) in the mapping file. To use the run prefix from the fasta label, such as 'FLP3FBN01ELBSX', where 'FLP3FBN01' is generated from the run ID, use 'run_prefix' and set the run prefix to be used as the data under the column header 'run_prefix'" optional="True"/>
-        <param argument="--suppress_html" type="boolean" label="Disable html file generation?" truevalue="-s" falsevalue="" checked="False" help="It can be useful for extremely large mapping files"/>
+        <param argument="--not_barcoded" type="boolean" truevalue="" falsevalue="--not_barcoded" checked="true" label="Are barcodes present?" help="BarcodeSequence header is still required in mapping file"/>
+        <param argument="--variable_len_barcodes" type="boolean" truevalue="" falsevalue="--variable_len_barcodes" checked="true" label="Are barcodes with variable length?"/>
+        <param argument="--disable_primer_check" type="boolean" truevalue="-disable_primer_check" falsevalue="" checked="false" label="Disable checks for primers?" help="LinkerPrimerSequence header is still required in mapping file"/>
+        <param argument="--added_demultiplex_field" type="text" optional="true" label="Field to use in the mapping file as additional demultiplexing (optional)" help="It can be used with or without barcodes. All combinations of barcodes/primers and these fields must be unique. The fields must contain values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'. In this case, 'plate' would be the column header and 'R_2008_12_09' would be the field data (minus quotes) in the mapping file. To use the run prefix from the fasta label, such as 'FLP3FBN01ELBSX', where 'FLP3FBN01' is generated from the run ID, use 'run_prefix' and set the run prefix to be used as the data under the column header 'run_prefix'"/>
+        <param argument="--suppress_html" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Disable html file generation?" help="It can be useful for extremely large mapping files"/>
     </inputs>
     <outputs>
         <data name="html_report" format="html" label="${tool.name} on ${on_string}: html report">