--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dedup_hash.xml	Wed Nov 23 07:49:05 2016 -0500
@@ -0,0 +1,114 @@
+<tool id="dedup_hash" name="Deduplicate FASTQ files" version="0.1.1">
+    <description>with fast and memory-efficient sequence hashes</description>
+    <requirements>
+        <requirement type="package" version="0.150.1">smhasher</requirement>
+    </requirements>
+    <command><![CDATA[
+    python '$__tool_directory__/dedup_hash/dedup_hash.py'
+    #if str($readtype.single_or_paired) == "se":
+        --r1_in '${readtype.input_single}'
+        --r1_out '$output_single'
+    #elif str($readtype.single_or_paired) == "pe_sep":
+        --r1_in '${readtype.input_paired1}'
+        --r2_in '${readtype.input_paired2}'
+        --r1_out '$output_paired1'
+        --r2_out '$output_paired2'
+    #else
+        --r1_in '${readtype.input_paired.forward}'
+        --r2_in '${readtype.input_paired.reverse}'
+        --r1_out '${output_paired_coll.forward}'
+        --r2_out '${output_paired_coll.reverse}'
+    #end if
+    $compress_fastq
+    ]]></command>
+    <inputs>
+        <conditional name="readtype">
+            <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
+                <option value="se" selected="true">Single-end</option>
+                <option value="pe_sep">Paired-end (two separate input files)</option>
+                <option value="pe_collection">Paired-end (as collection)</option>
+            </param>
+            <when value="se">
+                <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" />
+            </when>
+            <when value="pe_sep">
+                <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" />
+                <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" />
+            </when>
+            <when value="pe_collection">
+                <param name="input_paired" format="fastq,fastq.gz" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" />
+            </when>
+        </conditional>
+        <param name="compress_fastq" type="boolean" checked="true" truevalue="--write_gzip" falsevalue="" label="Produce compressed fastq?"/>
+    </inputs>
+    <outputs>
+        <data name="output_single" format="fastq" label="Single-end output of ${tool.name} on ${on_string}">
+            <filter>readtype['single_or_paired'] == 'se'</filter>
+            <change_format>
+                <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
+            </change_format>
+        </data>
+        <data name="output_paired1" format="fastq" label="Paired-end forward strand output of ${tool.name} on ${on_string}">
+            <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
+            <change_format>
+                <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
+            </change_format>
+        </data>
+        <data name="output_paired2" format="fastq" label="Paired-end reverse strand output of ${tool.name} on ${on_string}">
+            <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
+            <change_format>
+                <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
+            </change_format>
+        </data>
+        <collection name="output_paired_coll" type="paired" structured_like="readtype.pe_collection" label="Paired-end output of ${tool.name} on ${on_string}">
+            <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
+            <data name="forward" format="fastq">
+                <change_format>
+                    <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
+                </change_format>
+            </data>
+            <data name="reverse" format="fastq">
+                <change_format>
+                    <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
+                </change_format>
+            </data>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="single_or_paired" value="pe_sep"/>
+            <param name="input_paired1" value="r1.fastq.gz" ftype="fastq.gz"/>
+            <param name="input_paired2" value="r2.fastq.gz" ftype="fastq.gz"/>
+            <param name="compress_fastq" value="--write_gzip"/>
+            <output name="output_paired1" file="r1_dedup.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
+            <output name="output_paired2" file="r2_dedup.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="single_or_paired" value="pe_sep"/>
+            <param name="input_paired1" value="r1.fastq" ftype="fastq"/>
+            <param name="input_paired2" value="r2.fastq" ftype="fastq"/>
+            <param name="compress_fastq" value=""/>
+            <output name="output_paired1" file="r1_dedup.fastq" ftype="fastq"/>
+            <output name="output_paired2" file="r2_dedup.fastq" ftype="fastq"/>
+        </test>
+    </tests>
+    <help> <![CDATA[
+**Deduplicate paired fastq** is a fast and memory-efficient tool for removal of duplicates in paired short DNA sequence reads in fastq format.
+It identifies duplicates by concatenating the sequence of a readpair and calculating a short hash that uniquely identifies the concatenated sequence.
+Sequences that are not unique (i.e a hash of the concatenated sequence has been seen previously) are being discarded.
+
+Compared to fastuniq this tool requires only a fraction of the memory, but does not identify pairs that are identical,
+except for a switch of R1 and R2. Such reads may nevertheless align to different places based on the seed-searching of the aligner,
+so this may or may not be a problem for your application.
+
+Fastuniq consumed 76 GB of memory and took 4:01.52 on a typical dataset of 100nt 25 x 10^6 paired end reads,
+while this tool took 4.7GB of memory and 3:23.27 for the same dataset.
+
+Both tools produced the exact same result, arguing that, at least before quality and/or adapter trimming,
+the previously mentioned limitations are of theoretical concern.
+
+     ]]> </help>
+    <citations>
+        <citation type="doi">doi:10.1371/journal.pone.0052249</citation>
+    </citations>
+</tool>