--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_libraries_fastq.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,239 @@
+<tool id="split_libraries_fastq" name="Split fastq libraries" version="1.9.1">
+    <description>to performs demultiplexing of Fastq sequence data</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        split_libraries_fastq.py --version
+    ]]>
+    </version_command>
+
+    <command><![CDATA[
+        split_libraries_fastq.py
+
+            #set $seq_files = ''
+            #set $sep = ''
+            #for $file in $input_fastq_files 
+                #set $seq_files += $sep + str($file)
+                #set $sep = ','
+            #end for
+            -i $seq_files
+
+            -o split_libraries
+
+            #set $mapping_files = ''
+            #set $sep = ''
+            #for $file in $input_mapping_files 
+                #set $mapping_files += $sep + str($file)
+                #set $sep = ','
+            #end for
+            -m $mapping_files
+
+            #set $barcode_files = ''
+            #set $sep = ''
+            #for $file in $input_files_barcode_read_fps 
+                #set $barcode_files += $sep + str($file)
+                #set $sep = ','
+            #end for
+            -b $barcode_files
+
+            $store_qual_scores
+
+            #if str($sample_ids):
+                --sample_ids $sample_ids
+            #end if
+
+            $store_demultiplexed_fastq
+            $retain_unassigned_reads
+            -r $max_bad_run_length
+            -p $min_per_read_length_fraction
+            -n $sequence_max_n
+            -s $start_seq_id
+
+            $rev_comp_barcode
+            $rev_comp_mapping_barcodes
+            $rev_comp
+
+            -q $phred_quality_threshold
+            
+            #if str( $barcode_type.barcode_selector ) != "custom_length"
+                --barcode_type $barcode_type.barcode_selector
+            #else
+                --barcode_type $barcode_type.barcode_length
+            #end if
+
+            --max_barcode_errors $max_barcode_errors
+
+            $phred_offset
+]]>
+    </command>
+
+	<inputs>
+        <param name="input_fastq_files" type="data" 
+            format="fastq,fastqsanger,fastqsolexa" 
+            label="Input fastq files" multiple="True" help="(-i/--sequence_read_fps)"/> 
+
+		<param name="input_mapping_files" type="data" 
+            format="txt,tabular,tsv,csv" label="Metadata mapping files (optional)" 
+            multiple="True" optional="True" help="(-m/--mapping_fps)"/> 
+
+        <param name="input_files_barcode_read_fps" type="data" 
+            format="fastq,fastqsanger,fastqsolexa" label="Barcode read files (optional)" 
+            multiple="True" optional="True" help="(-b/--barcode_read_fps)"/> 
+
+		<param name="store_qual_scores" type="boolean" label="Store quality strings
+            in files?" truevalue="--store_qual_scores" falsevalue="" checked="False" 
+            help="(--store_qual_scores)" />
+
+        <param name="sample_ids" type="text" label="Comma-separated list of samples 
+            ids to be applied to all sequences (optional)" optional="True" 
+            help="It must be one per input file path (used when data is not 
+            multiplexed, --sample_ids)"/> 
+
+        <param name="store_demultiplexed_fastq" type="boolean" label="Write
+            demultiplexed fastq files?" truevalue="--store_demultiplexed_fastq" 
+            falsevalue="" checked="False" help="(--store_demultiplexed_fastq)" />
+
+        <param name="retain_unassigned_reads" type="boolean" label="Retain 
+            sequences which don’t map to a barcode in the mapping file?" 
+            truevalue="--retain_unassigned_reads" falsevalue="" checked="False" 
+            help="Sample ID will be 'Unassigned' (--retain_unassigned_reads)" />
+
+        <param name="max_bad_run_length" type="integer" value="3"
+            label="Maximum number of consecutive low quality base calls allowed 
+            before truncating a read" help="(-r/--max_bad_run_length)" />
+
+        <param name="min_per_read_length_fraction" type="float" value="0.75"
+            label="Minimum number of consecutive high quality base calls to 
+            include a read (per single end read) as a fraction of the input read 
+            length" help="(-p/--min_per_read_length_fraction)" />
+
+        <param name="sequence_max_n" type="integer" value="0"
+            label="Maximum number of N characters allowed in a sequence to retain 
+            it" help="This is applied after quality trimming, and is total over 
+            combined paired end reads if applicable (-n/--sequence_max_n)" />
+
+        <param name="start_seq_id" type="integer" value="0"
+            label="Start seq_ids as ascending integers beginning with start_seq_id" 
+            help="(-s/--start_seq_id)" />
+
+        <param name="rev_comp_barcode" type="boolean" label="Reverse complement 
+            barcode reads before lookup?" truevalue="--rev_comp_barcode" 
+            falsevalue="" checked="False" help="(--rev_comp_barcode)" />
+
+        <param name="rev_comp_mapping_barcodes" type="boolean" label="Reverse 
+            complement barcode in mapping before lookup?" 
+            truevalue="--rev_comp_mapping_barcodes" falsevalue="" checked="False" 
+            help="It is useful if barcodes in mapping file are reverse 
+            complements of golay codes (--rev_comp_mapping_barcodes)" />
+
+        <param name="rev_comp" type="boolean" label="Reverse omplement sequence 
+            before writing to output file?" truevalue="--rev_comp" falsevalue="" 
+            checked="False" help="(--rev_comp)" />
+
+        <param name="phred_quality_threshold" type="integer" value="3"
+            label="Maximum unacceptable Phred quality score" help="E.g., for
+            Q20 and better, 19 must be specified (-q/--phred_quality_threshold)" />
+		
+		<conditional name="barcode_type">
+            <param name="barcode_selector" type="select" label="Type of barcode"
+                help="(--barcode_type)">
+                <option value="hamming_8">hamming_8</option>
+                <option value="golay_12" selected="true">golay_12</option>
+                <option value="variable_length">variable_length (disable any barcode correction)</option>
+                <option value="custom_length">Custom length</option>
+                <option value="not-barcoded">Data not barcoded</option>
+            </param>
+            <when value="hamming_8" />
+            <when value="golay_12" />
+            <when value="variable_length" />
+            <when value="custom_length">
+                <param name="barcode_length" type="integer" value="4" 
+                label="Barcode length"/>
+            </when>
+            <when value="not-barcoded" />
+        </conditional>
+
+        <param name="max_barcode_errors" type="float" value="1.5"
+            label="Maximum number of errors in barcode" 
+            help="(--max_barcode_errors)" />
+
+        <param name="phred_offset" type="select" label="Ascii offset to use when 
+            decoding phred scores" help="(--phred_offset)">
+            <option value="--phred_offset 33">33</option>
+            <option value="--phred_offset 64">64</option>
+            <option value="" selected="true">Automatically determined</option>
+        </param>
+    </inputs>
+
+	<outputs>
+		<data name="log" format="txt" 
+            from_work_dir="split_libraries/split_library_log.txt"
+            label="${tool.name} on ${on_string}: log"/>
+        <data name="histograms" format="tabular" 
+            from_work_dir="split_libraries/histograms.txt"
+            label="${tool.name} on ${on_string}: histograms"/>
+        <data name="seqs" format="fasta" 
+            from_work_dir="split_libraries/seqs.fna"
+            label="${tool.name} on ${on_string}: sequences"/>
+        <data name="seqs_qual" format="qual" 
+            from_work_dir="split_libraries/seqs.qual"
+            label="${tool.name} on ${on_string}: sequence qualities">
+            <filter>store_qual_scores is True</filter>
+        </data>
+        <data name="seqs_fastq" format="fastq"
+            from_work_dir="split_libraries/seqs.fastq"
+            label="${tool.name} on ${on_string}: demultiplexed sequences (fastq)">
+            <filter>store_demultiplexed_fastq is True</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_fastq_files" value="forward_reads.fastq"/>
+            <param name="input_mapping_files" value="map.tsv"/>
+            <param name="input_files_barcode_read_fps" value="barcodes.fastq"/>
+            <param name="store_qual_scores" value="--store_qual_scores" />
+            <param name="store_demultiplexed_fastq" value="--store_demultiplexed_fastq" />
+            <param name="retain_unassigned_reads" value=""/>
+            <param name="max_bad_run_length" value="3"/>
+            <param name="min_per_read_length_fraction" value="0.75"/>
+            <param name="sequence_max_n" value="0"/>
+            <param name="start_seq_id" value="0" />
+            <param name="rev_comp_barcode" value="" />
+            <param name="rev_comp_mapping_barcodes" value="" />
+            <param name="rev_comp" value="" />
+            <param name="start_seq_id" value="3"/>
+            <param name="barcode_selector" value="golay_12"/>
+            <param name="max_barcode_errors" value="1.5"/>
+            <param name="phred_offset" value="" />
+
+            <output name="log" file="split_fastq_libraries_log.txt"/>
+            <output name="seqs" file="split_fastq_libraries_sequences.fasta"/>
+            <output name="histograms" file="split_fastq_libraries_histograms.tabular"/>
+            <output name="histograms" file="split_fastq_libraries_histograms.tabular"/>
+            <output name="seqs_qual" file="split_fastq_libraries_sequence_qualities.qual"/>
+            <output name="seqs_fastq" file="split_fastq_libraries_demultiplexed_sequences.fastq"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+This tool performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).
+
+More information about this tool is available on 
+`QIIME documentation <http://qiime.org/scripts/split_libraries_fastq.html>`_.
+]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+
+</tool>