--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/validate_mapping_file.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,145 @@
+<tool id="qiime_validate_mapping_file" name="Validate mapping file" version="1.9.1">
+    <description>to check for required data and format</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        validate_mapping_file.py --version
+    ]]></version_command>
+
+    <command><![CDATA[
+        validate_mapping_file.py 
+            -m $mapping_fp 
+            -o validate_mapping_file_output
+            $verbose
+            -c $char_replace
+            $not_barcoded
+            $variable_len_barcodes
+            $disable_primer_check
+
+            #if str($added_demultiplex_field):
+                -j $added_demultiplex_field
+            #end if
+
+            $suppress_html
+
+        #if not $suppress_html:
+            &&
+            mkdir -p $html_report.files_path 
+            &&
+            cp validate_mapping_file_output/*.html $html_report.files_path  
+            &&
+            cp "validate_mapping_file_output/overlib.js" "$html_report.extra_files_path"
+            &&
+            mv $html_report.files_path/*.html $html_report
+        #end if
+]]>
+    </command>
+
+	<inputs>
+		<param name="mapping_fp" label="Metadata mapping filepath" type="data" 
+            format="tabular,csv,txt,tsv" help="(-m/--mapping_fp)"/>
+
+        <param name="verbose" type="boolean" label="Enable printing information 
+            to standard out?" truevalue="-v" falsevalue="" checked="False" 
+            help="(-v/--verbose)" />
+
+		<param name="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). 
+            (-c/--char_replace)"/>
+
+		<param name="not_barcoded" type="boolean" label="Are barcodes present?" 
+            truevalue="" falsevalue="--not_barcoded" checked="True" 
+            help="BarcodeSequence header is still required in mapping file 
+            (-b/--not_barcoded)"/>
+
+        <param name="variable_len_barcodes" type="boolean" label="Are barcodes with
+            variable length?" truevalue="" falsevalue="--variable_len_barcodes" 
+            checked="True" help="(-B/--variable_len_barcodes)"/>
+
+        <param name="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 (-p/--disable_primer_check)"/>
+
+		<param name="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' (-j/--added_demultiplex_field)" optional="True"/>
+
+        <param name="suppress_html" type="boolean" label="Disable html file 
+            generation?" truevalue="-s" falsevalue="" checked="False" 
+            help="It can be useful for extremely large mapping files 
+            (-s/--suppress_html)"/>
+    </inputs>
+
+	<outputs>
+        <data name="html_report" format="html" 
+            label="${tool.name} on ${on_string}: html report">
+            <filter>suppress_html is False</filter>
+        </data>
+		<data name="log" format="txt"
+            from_work_dir="validate_mapping_file_output/*.log"
+            label="${tool.name} on ${on_string}: log"/>
+        <data format="tabular" name="mapping_fp_corrected" 
+            from_work_dir="validate_mapping_file_output/*corrected.txt"
+            label="${tool.name} on ${on_string}: corrected map" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="mapping_fp" value="map.tsv"/>
+            <param name="verbose" value="" />
+            <param name="char_replace" value="_" />
+            <param name="not_barcoded" value="" />
+            <param name="variable_len_barcodes" value="" />
+            <param name="disable_primer_check" value="" />
+            <param name="suppress_html" value="" />
+
+            <output name="log" file="validate_mapping_file_log.txt"/>
+            <output name="mapping_fp_corrected" 
+                file="validate_mapping_file_corrected_map.tabular"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does?**
+
+This tool checks user’s metadata mapping file for required data, valid format
+
+Specifically, it checks that:
+
+    - The BarcodeSequence, LinkerPrimerSequences, and ReversePrimer fields have valid IUPAC DNA characters, and BarcodeSequence characters are non-degenerate (error)
+    - The SampleID, BarcodeSequence, LinkerPrimerSequence, and Description headers are present. (error)
+    - There are not duplicate header fields (error)
+    - There are not duplicate barcodes (error)
+    - Barcodes are of the same length.  Suppressed when variable_len_barcode flag is passed (warning)
+    - The headers do not contain invalid characters (alphanumeric and underscore only) (warning)
+    - The data fields do not contain invalid characters (alphanumeric, underscore, space, and +-%./:,; characters) (warning)
+    - SampleID fields are MIENS compliant (only alphanumeric and . characters). (warning)
+    - There are no duplicates when the primer and variable length barcodes are appended (error)
+    - There are no duplicates when barcodes and added demultiplex fields (-j option) are combined (error)
+    - Data fields are not found beyond the Description column (warning)
+
+More information about this tool is available on 
+`QIIME documentation <http://qiime.org/scripts/validate_mapping_file.html>`_.
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+
+</tool>