--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sync_reads.xml	Sat Mar 02 07:44:26 2024 +0000
@@ -0,0 +1,104 @@
+<tool id="b2b_sync_reads" name="Sync paired reads" version="0.005">
+
+    <description>Synchronize trimmed/filtered read-pair set</description>
+
+    <!-- ***************************************************************** -->
+
+    <requirements>
+        <requirement type="package" version="0.019">b2b-utils</requirement>
+    </requirements>
+
+    <!-- ***************************************************************** -->
+
+    <version_command>sync_reads --version | perl -wnE'print "$1\n" for /sync_reads v(.+)/g'</version_command>
+
+    <!-- ***************************************************************** -->
+
+    <command detect_errors="aggressive">
+    <![CDATA[
+
+    sync_reads
+    --fwd $input1
+    --rev $input2
+    --fwd_out $fwd_out
+    --rev_out $rev_out
+    #if str($write_singles) == 'y':
+	--singles
+        --fwd_singles_out $fwd_s_out
+        --rev_singles_out $rev_s_out
+    #end if
+
+    ]]>
+    </command>
+
+    <!-- ***************************************************************** -->
+
+    <inputs>
+
+        <param name="job_name" type="text" size="120" value="sync_reads" label="Job narrative (added to output names)"
+          help="Only letters, numbers and underscores (_) will be retained in this field">
+           <sanitizer invalid_char="">
+              <valid initial="string.letters,string.digits"><add value="_" /> </valid>
+           </sanitizer>
+        </param>
+        <!-- FASTQ input(s) and options specifically for paired-end data. -->
+        <param name="input1" format="fastqsanger,fastq" type="data" label="Forward read FASTQ file" help="Forward read FASTQ file"/>
+        <param name="input2" format="fastqsanger,fastq" type="data" label="Reverse read FASTQ file" help="Reverse read FASTQ file"/>
+        <param name="write_singles" type="boolean" label="Output singletons" checked="False" truevalue="y" falsevalue="n" />
+
+    </inputs>
+
+    <!-- ***************************************************************** -->
+
+    <outputs>
+        <data format_source="input1" name="fwd_out" label="${job_name}_sync.1.fq" />
+        <data format_source="input2" name="rev_out" label="${job_name}_sync.2.fq" />
+        <data format_source="input1" name="fwd_s_out" label="${job_name}_singles.1.fq">
+            <filter>write_singles</filter>
+        </data>
+        <data format_source="input2" name="rev_s_out" label="${job_name}_singles.2.fq">
+            <filter>write_singles</filter>
+        </data>
+    </outputs>
+
+    <!-- ***************************************************************** -->
+
+    <tests>
+
+        <test expect_num_outputs="2">
+            <param name="input1" value="test_R1.fq" ftype="fastq" />
+            <param name="input2" value="test_R2.fq" ftype="fastq" />
+            <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
+            <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
+        </test>
+
+        <test expect_num_outputs="4">
+            <param name="input1" value="test_R1.fq" ftype="fastq" />
+            <param name="input2" value="test_R2.fq" ftype="fastq" />
+            <param name="write_singles" value="True" />
+            <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
+            <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
+            <output name="fwd_s_out" file="test_R1.singles.fq" compare="diff" />
+            <output name="rev_s_out" file="test_R2.singles.fq" compare="diff" />
+        </test>
+
+    </tests>
+
+    <!-- ***************************************************************** -->
+
+    <help>
+
+    sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
+    reverse FASTQ read files. It will output a new pair of files containing only
+    read pairs found in both input files. It can optionally output singletons from
+    each input file as well.
+
+    </help>
+
+    <!-- ***************************************************************** -->
+
+    <citations>
+    </citations>
+
+</tool>
+