--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_families.xml	Mon Nov 23 22:06:21 2015 -0500
@@ -0,0 +1,83 @@
+<?xml version="1.0"?>
+<tool id="make_families" name="Make families" version="0.1">
+  <description>from duplex sequencing data</description>
+  <requirements>
+    <requirement type="package" version="0.1">duplex</requirement>
+    <requirement type="set_environment">DUPLEX_DIR</requirement>
+  </requirements>
+  <command>paste $fastq1 $fastq2
+    | paste - - - -
+    | awk -f \$DUPLEX_DIR/make-barcodes.awk -v TAG_LEN=$taglen -v INVARIANT=$invariant
+    | sort
+    &gt; $output
+  </command>
+  <inputs>
+    <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/>
+    <param name="fastq2" type="data" format="fastq" label="Sequencing reads, mate 2"/>
+    <param name="taglen" type="integer" value="12" min="0" label="Tag length" help="length of each random barcode on the ends of the fragments"/>
+    <param name="invariant" type="integer" value="5" min="0" label="Invariant sequence length" help="length of the sequence between the tag and actual sample sequence (the restriction site, normally)"/>
+  </inputs>
+  <outputs>
+    <data name="output" format="tabular"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="fastq1" value="smoke_1.fq"/>
+      <param name="fastq2" value="smoke_2.fq"/>
+      <param name="taglen" value="5"/>
+      <param name="invariant" value="1"/>
+      <output name="output" file="smoke.families.tsv"/>
+    </test>
+    <test>
+      <param name="fastq1" value="smoke_1.fq"/>
+      <param name="fastq2" value="smoke_2.fq"/>
+      <param name="taglen" value="5"/>
+      <param name="invariant" value="0"/>
+      <output name="output" file="smoke.families.i0.tsv"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This tool is for processing raw duplex sequencing data, removing the barcodes and grouping by them into families of reads from the same fragment.
+
+-----
+
+**Output**
+
+The output will be a tabular file where each line corresponds to a pair of input reads.
+
+The columns are::
+
+  1: barcode (both tags joined and ordered)
+  2: tag order in barcode ("ab" or "ba")
+  3: read1 name
+  4: read1 sequence (minus the tag and invariant sequences)
+  5: read1 quality scores (minus the same tag and invariant)
+  6: read2 name
+  7: read2 sequence (minus the tag and invariant sequences)
+  8: read2 quality scores (minus the same tag and invariant)
+
+-----
+
+**Barcode creation**
+
+For each pair, the tool will remove the tag at the beginning of each read and create a barcode by concatenating the two tags. The order of the tags is determined by a string comparison so that it will make an identical barcode from pairs of either order. The original tag order will be noted in the second column.
+
+Since pairs from opposite strands will have the same tags, but in the reverse order, this produces the same barcode for reads from the same fragment, regardless of strand. Then a simple sort will group all reads from the same strand together, separated into strands by the different "order" values.
+
+Examples::
+
+  +---------------+-----------------+
+  |  input tags   |     output      |
+  +-------+-------+-------+---------+
+  | read1 | read2 | order | barcode |
+  +-------+-------+-------+---------+
+  |  ATG  |  CCT  |  ab   | ATGCCT  |
+  +-------+-------+-------+---------+
+  |  CCT  |  ATG  |  ba   | ATGCCT  |
+  +-------+-------+-------+---------+
+
+    </help>
+</tool>