# HG changeset patch
# User rdvelazquez
# Date 1553269369 14400
# Node ID 85d823cf087288875f2954d7ba04b08fd33ee1fe
# Parent  d91cbcdac691627a527361c6b0664d8be296c7eb
planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty

diff -r d91cbcdac691 -r 85d823cf0872 bealign.xml
--- a/bealign.xml	Thu Apr 19 12:10:57 2018 -0400
+++ b/bealign.xml	Fri Mar 22 11:42:49 2019 -0400
@@ -1,134 +1,115 @@
 <?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[
+  <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>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[
-  -r REFERENCE, --reference REFERENCE
-                        REFERENCE FASTA file or {HXB2_tat, HXB2_nef, HXB2_vpu,
-                        HXB2_vif, HXB2_env, HXB2_vpr, HXB2_rev, HXB2_pol,
-                        HXB2_prrt, NL4-3_prrt, HXB2_rt, HXB2_gag, HXB2_pr,
-                        HXB2_int}
-  -e EXPECTED_IDENTITY, --expected-identity EXPECTED_IDENTITY
-                        discard sequences that are insufficiently identical to
-                        the reference
-  -a ALPHABET, --alphabet ALPHABET
-                        perform an alignment using one of {amino, dna, codon}
-                        [default=codon]
-  -m SCOREMATRIX, --score-matrix SCOREMATRIX
-                        parameterize using one of {PAM250, DNA80,
-                        HIV_BETWEEN_F, BLOSUM62, DNA70, DNA88, PAM200, DNA95,
-                        DNA65} [default=BLOSUM62]
-  -D DISCARD, --discard DISCARD
-                        discarded sequences are sent to DISCARD
-  -R, --reverse-complement
-                        also align the reverse complement of each query
-                        sequence, returning it if the alignment is superior
-  -S, --no-sort         do NOT sort the resulting BAM file [the default is to
-                        sort]
-  -q, --quiet           do not print status update messages
-  -v, --version         print version information and exit
-  -K, --keep-reference  include the reference sequence as the first one in the
-                        resulting BAM file [the default is to strip it]
+        '$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 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>
diff -r d91cbcdac691 -r 85d823cf0872 test-data/bealign-out1.bam
Binary file test-data/bealign-out1.bam has changed
diff -r d91cbcdac691 -r 85d823cf0872 test-data/bealign-out2.bam
Binary file test-data/bealign-out2.bam has changed
diff -r d91cbcdac691 -r 85d823cf0872 test-data/bealign-out3.bam
Binary file test-data/bealign-out3.bam has changed