--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bealign.xml	Wed May 16 17:34:42 2018 -0400
@@ -0,0 +1,117 @@
+<?xml version="1.0"?>
+<tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0">
+    <description>to a reference using a codon alignment algorithm</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command>bealign --version</version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+    bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
+        #if $advanced.expected_identity:
+            --expected-identity $advanced.expected_identity
+        #end if
+        --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
+        #if $advanced.discard:
+            $advanced.discard '$advanced.discarded_reads'
+        #end if
+        '$input' '$output'
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Input reads" />
+        <conditional name="select_reference">
+            <param name="reference_type" type="select">
+                <option value="preset">Select preset</option>
+                <option value="dataset">Use a history dataset</option>
+            </param>
+            <when value="preset">
+                <param argument="--reference" type="select">
+                    <option value="HXB2_tat">HXB2 tat</option>
+                    <option value="HXB2_gag">HXB2 gag</option>
+                    <option value="HXB2_pol">HXB2 polymerase</option>
+                    <option value="HXB2_int">HXB2 integrase</option>
+                    <option value="HXB2_vif">HXB2 vif</option>
+                    <option value="HXB2_pr">HXB2 protease</option>
+                    <option value="HXB2_vpr">HXB2 vpr</option>
+                    <option value="NL4-3_prrt">NL4-3 protease and reverse transcriptase</option>
+                    <option value="HXB2_nef">HXB2 nef</option>
+                    <option value="HXB2_env">HXB2 envelope</option>
+                    <option value="HXB2_rt">HXB2 reverse transcriptase</option>
+                    <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option>
+                    <option value="HXB2_rev">HXB2 rev</option>
+                    <option value="HXB2_vpu">HXB2 vpu</option>
+                </param>
+            </when>
+            <when value="dataset">
+                <param argument="--reference" type="data" format="fasta" label="Reference sequences" />
+            </when>
+        </conditional>
+        <section name="advanced" title="Advanced options" expanded="False">
+            <param name="expected_identity" argument="--expected-identity" type="float" min="0" max="1" optional="True" label="Discard sequences that are insufficiently identical to the reference" />
+            <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
+                <option value="codon" selected="True">Codon</option>
+                <option value="dna">DNA</option>
+                <option value="amino">Amino acids</option>
+            </param>
+            <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
+                <option value="BLOSUM62" selected="True">Blocks substitution</option>
+                <option value="DNA65">DNA, 65% expected identity</option>
+                <option value="DNA70">DNA, 70% expected identity</option>
+                <option value="DNA88">DNA, 88% expected identity</option>
+                <option value="DNA80">DNA, 80% expected identity</option>
+                <option value="DNA95">DNA, 95% expected identity</option>
+                <option value="PAM200">PAM 200 substitution</option>
+                <option value="PAM250">PAM 250 substitution</option>
+                <option value="HIV_BETWEEN_F">HIV between+F</option>
+            </param>
+            <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
+            <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" />
+            <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="bam" />
+        <data name="discarded_reads" format="fasta">
+            <filter>advanced['discard']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="fasta" value="bealign-in1.fa" />
+            <param name="reference_type" value="dataset" />
+            <param name="score_matrix" value="HIV_BETWEEN_F" />
+            <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" />
+            <output name="output" file="bealign-out1.bam" />
+        </test>
+        <test>
+            <param name="input" ftype="fasta" value="bealign-in2.fa" />
+            <param name="reference_type" value="dataset" />
+            <param name="score_matrix" value="BLOSUM62" />
+            <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
+            <output name="output" file="bealign-out2.bam" />
+        </test>
+        <test>
+            <param name="input" ftype="fasta" value="bealign-in2.fa" />
+            <param name="reference_type" value="dataset" />
+            <param name="expected_identity" value="0.9" />
+            <param name="score_matrix" value="BLOSUM62" />
+            <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
+            <output name="output" file="bealign-out3.bam" />
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+bealign
+-------
+
+Align sequences to a reference using a codon alignment algorithm.
+
+NOTES
+-----
+
+Reference can be one of the presets or a custom history reference.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>