--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prestor_abseq3.xml	Wed May 30 15:35:10 2018 -0400
@@ -0,0 +1,79 @@
+<tool id="prestor_abseq3" name="pRESTOr AbSeq3 Report" version="@PRESTO_VERSION@">
+    <description>Create HTML QC report from pRESTO outputs</description>
+    
+    <macros>
+        <import>presto_macros.xml</import>
+    </macros>
+    
+    <requirements>
+          <requirement type="package" version="07f9c7caeb60">prestor</requirement>
+    </requirements>
+    
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$qual1'    ./quality-1_table.tab &&
+        ln -s '$qual2'    ./quality-2_table.tab &&
+        ln -s '$primer1'  ./primers-1_table.tab &&
+        ln -s '$primer2'  ./primers-2_table.tab &&
+        ln -s '$cons1'    ./consensus-1_table.tab &&
+        ln -s '$cons2'    ./consensus-2_table.tab &&
+        ln -s '$assemble' ./assemble_table.tab &&
+        ln -s '$maskqual' ./maskqual_table.tab &&
+        ln -s '$cregion'  ./cregion_table.tab &&
+        Rscript '${prestor_script}'
+    ]]></command>
+    
+    <configfiles>
+        <configfile name="prestor_script"><![CDATA[
+library(prestor)
+report_abseq3('.', sample='${sample}', output_dir='.', output_file='report.html', format='html')
+        ]]>
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param name="sample" type="text" label="Sample Name" help="Sample Name. Must not contain spaces.">
+            <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[^\s]+</validator>
+        </param>
+        <param name="qual1" type="data" format="txt" label="ParseLog of FilterSeq(R1)" help="Output of running ParseLog on the log file from FilterSeq on Read 1."/>
+        <param name="qual2" type="data" format="txt" label="ParseLog of FilterSeq(R2)" help="Output of running ParseLog on the log file from FilterSeq on Read 2."/>
+        <param name="primer1" type="data" format="txt" label="ParseLog of MaskPrimers(R1)" help="Output of running ParseLog on the log file from MaskPrimers on Read 1."/>
+        <param name="primer2" type="data" format="txt" label="ParseLog of MaskPrimers(R2)" help="Output of running ParseLog on the log file from MaskPrimers on Read 2."/>
+        <param name="cons1" type="data" format="txt" label="ParseLog of BuildConsensus(R1)" help="Output of running ParseLog on the log file from BuildConsensus on Read 1."/>
+        <param name="cons2" type="data" format="txt" label="ParseLog of BuildConsensus(R2)" help="Output of running ParseLog on the log file from BuildConsensus on Read 2."/>
+        <param name="assemble" type="data" format="txt" label="ParseLog of AssemblePairs" help="Output of running ParseLog on the log file from AssemblePairs."/>
+        <param name="maskqual" type="data" format="txt" label="ParseLog of FilterSeq(pairs)" help="Output of running ParseLog on the log file from FilterSeq on the consensus reads."/>
+        <param name="cregion" type="data" format="txt" label="ParseLog of MaskPrimers(pairs)" help="Output of running ParseLog on the log file from MaskPrimers for the C Region."/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="html" from_work_dir="report.html"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param  name="sample" value="TestSample"/>
+            <param  name="qual1" value="prestor_logs/quality-1_table.tab"/>
+            <param  name="qual2" value="prestor_logs/quality-2_table.tab"/>
+            <param  name="primer1" value="prestor_logs/primers-1_table.tab"/>
+            <param  name="primer2" value="prestor_logs/primers-2_table.tab"/>
+            <param  name="cons1" value="prestor_logs/consensus-1_table.tab"/>
+            <param  name="cons2" value="prestor_logs/consensus-2_table.tab"/>
+            <param  name="assemble" value="prestor_logs/assemble_table.tab"/>
+            <param  name="maskqual" value="prestor_logs/maskqual_table.tab"/>
+            <param  name="cregion" value="prestor_logs/cregion_table.tab"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="pRESTO Report"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Creates an HTML QC report from the log files generated when running pRESTO.
+
+See the `Prestor project page <https://bitbucket.org/javh/prototype-prestor/src>`_ for more information.
+    ]]></help>
+    
+    <expand macro="citations" />
+</tool>