--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/presto_pairseq.xml	Wed May 30 15:37:15 2018 -0400
@@ -0,0 +1,62 @@
+<tool id="presto_pairseq" name="pRESTO PairSeq" version="@PRESTO_VERSION@">
+    <description>Sorts and matches sequence records with matching coordinates across files</description>
+    
+    <macros>
+        <import>presto_macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+    
+    <version_command>PairSeq.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$r1_in' r1.fastq &&
+        ln -s '$r2_in' r2.fastq &&
+        PairSeq.py
+          -1 r1.fastq
+          -2 r2.fastq
+          --coord $coord
+          #if $r1_annotations
+          --1f $r1_annotations
+          #end if
+          #if $r2_annotations
+          --2f $r2_annotations
+          #end if
+          --outdir=.
+          --outname=tmp
+    ]]></command>
+    <inputs>
+        <param argument="-1" name="r1_in" type="data" format="fastq" label="Read 1 FASTQ/FASTA file."/>
+        <param argument="-2" name="r2_in" type="data" format="fastq" label="Read 2 FASTQ/FASTA file."/>
+        <param argument="--1f" name="r1_annotations" type="text" optional="true" label="Annotation(s) to copy from R1 to R2." help="Multiple annotation must be space-separated.">
+            <expand macro="text-regex-validator"/>
+        </param>
+        <param argument="--2f" name="r2_annotations" type="text" optional="true" label="Annotation(s) to copy from R2 to R1." help="Multiple annotation must be space-separated.">
+            <expand macro="text-regex-validator"/>
+        </param>
+        <expand macro="presto-coord-param"/>
+    </inputs>
+    <outputs>
+        <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq"/>
+        <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
+            <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
+            <param name="r2_annotations" value="BARCODE"/>
+            <param name="coord" value="illumina"/>
+            <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
+            <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Sorts and matches sequence records with matching coordinates across files.
+
+See the `pRESTO online help <@PRESTO_URL_BASE@/PairSeq.html>`_ for more information.
+
+@HELP_NOTE@
+    ]]></help>
+    <expand macro="citations" />
+</tool>