# HG changeset patch
# User iuc
# Date 1625843945 0
# Node ID d8b6f0adaa79e03de2edeb727eb7a929fdc1a849
# Parent  f9b72a376ec9e978edb8c9e8eec8e87a7656408b
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"

diff -r f9b72a376ec9 -r d8b6f0adaa79 bealign.xml
--- a/bealign.xml	Thu May 13 16:57:26 2021 +0000
+++ b/bealign.xml	Fri Jul 09 15:19:05 2021 +0000
@@ -1,8 +1,9 @@
 <?xml version="1.0"?>
-<tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0">
+<tool id="bioext_bealign" name="Align sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>to a reference using a codon alignment algorithm</description>
     <macros>
         <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <expand macro="requirements" />
     <version_command>bealign --version</version_command>
@@ -51,6 +52,34 @@
                     <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option>
                     <option value="HXB2_rev">HXB2 rev</option>
                     <option value="HXB2_vpu">HXB2 vpu</option>
+                    <option value="CoV2-3C">SARS-CoV-2: 3C</option>
+                    <option value="CoV2-S">SARS-CoV-2: Spike</option>
+                    <option value="CoV2-E">SARS-CoV-2: Envelope</option>
+                    <option value="CoV2-M">SARS-CoV-2: Membrane</option>
+                    <option value="CoV2-N">SARS-CoV-2: Nucleoprotein</option>
+                    <option value="CoV2-endornase">SARS-CoV-2: endornase</option>
+                    <option value="CoV2-exonuclease">SARS-CoV-2: exonuclease</option>
+                    <option value="CoV2-helicase">SARS-CoV-2: helicase</option>
+                    <option value="CoV2-leader">SARS-CoV-2: leader</option>
+                    <option value="CoV2-methyltransferase">SARS-CoV-2: methyltransferase</option>
+                    <option value="CoV2-nsp2">SARS-CoV-2: nsp2</option>
+                    <option value="CoV2-nsp3">SARS-CoV-2: nsp3</option>
+                    <option value="CoV2-nsp4">SARS-CoV-2: nsp4</option>
+                    <option value="CoV2-nsp6">SARS-CoV-2: nsp6</option>
+                    <option value="CoV2-nsp7">SARS-CoV-2: nsp7</option>
+                    <option value="CoV2-nsp8">SARS-CoV-2: nsp8</option>
+                    <option value="CoV2-nsp9">SARS-CoV-2: nsp9</option>
+                    <option value="CoV2-nsp10">SARS-CoV-2: nsp10</option>
+                    <option value="CoV2-ORF1a">SARS-CoV-2: ORF1a</option>
+                    <option value="CoV2-ORF1b">SARS-CoV-2: ORF1b</option>
+                    <option value="CoV2-ORF3a">SARS-CoV-2: ORF3a</option>
+                    <option value="CoV2-ORF5">SARS-CoV-2: ORF5</option>
+                    <option value="CoV2-ORF6">SARS-CoV-2: ORF6</option>
+                    <option value="CoV2-ORF7a">SARS-CoV-2: ORF7a</option>
+                    <option value="CoV2-ORF7b">SARS-CoV-2: ORF7b</option>
+                    <option value="CoV2-ORF8">SARS-CoV-2: ORF8</option>
+                    <option value="CoV2-ORF10">SARS-CoV-2: ORF10</option>
+                    <option value="CoV2-RdRp">SARS-CoV-2: RNA-dependent RNA polymerase</option>
                 </param>
             </when>
             <when value="dataset">
@@ -92,14 +121,14 @@
             <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" ftype="bam" />
+            <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" />
         </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" ftype="bam" />
+            <output name="output" file="bealign-out2.bam" ftype="bam" lines_diff="2"/>
         </test>
         <test>
             <param name="input" ftype="fasta" value="bealign-in2.fa" />
@@ -107,7 +136,7 @@
             <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" ftype="bam" />
+            <output name="output" file="bealign-out3.bam" ftype="bam" lines_diff="2"/>
         </test>
     </tests>
     <help>
diff -r f9b72a376ec9 -r d8b6f0adaa79 macros.xml
--- a/macros.xml	Thu May 13 16:57:26 2021 +0000
+++ b/macros.xml	Fri Jul 09 15:19:05 2021 +0000
@@ -1,9 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">0.19.7</token>
+    <token name="@TOOL_VERSION@">0.20.1</token>
+    <token name="@PROFILE@">20.05</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">python-bioext</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">python-bioext</requirement>
             <yield />
         </requirements>
     </xml>
diff -r f9b72a376ec9 -r d8b6f0adaa79 test-data/bam2msa-out1.fa
--- a/test-data/bam2msa-out1.fa	Thu May 13 16:57:26 2021 +0000
+++ b/test-data/bam2msa-out1.fa	Fri Jul 09 15:19:05 2021 +0000
@@ -1,4 +1,4 @@
->Z|JP|K03455|2036|DUPLICATE
+>Z_JP_K03455_2036_DUPLICATE_2
 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
 GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
 AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
@@ -26,7 +26,7 @@
 ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
 ------------------------------------------------------------
 ---------------------------------------------------------
->Z|JP|K03455|2036|DUPLICATE
+>Z_JP_K03455_2036_DUPLICATE_3
 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
 GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
 AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
@@ -54,7 +54,7 @@
 ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
 ------------------------------------------------------------
 ---------------------------------------------------------
->Z|JP|K03455|2036|DUPLICATE
+>Z_JP_K03455_2036_DUPLICATE_4
 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
 GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTAYCAGGG
 AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
@@ -82,7 +82,7 @@
 ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
 ------------------------------------------------------------
 ---------------------------------------------------------
->Z|JP|K03455|2036|DUPLICATE
+>Z_JP_K03455_2036_DUPLICATE_5
 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
 GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
 AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAGGTAAGACAATATGAT
@@ -110,7 +110,7 @@
 ------------------------------------------------------------
 ------------------------------------------------------------
 ---------------------------------------------------------
->Z|JP|K03455|2036|DUPLICATE
+>Z_JP_K03455_2036_DUPLICATE_6
 CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
 GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
 AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGAT
@@ -138,7 +138,7 @@
 ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
 ------------------------------------------------------------
 ---------------------------------------------------------
->Z|JP|K03455|2036|DUPLICATE
+>Z_JP_K03455_2036_DUPLICATE_7
 CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
 GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA
 AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
@@ -166,7 +166,7 @@
 ATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGG
 TGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCC
 TTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC
->Z|JP|K03455|2036
+>Z_JP_K03455_2036
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
diff -r f9b72a376ec9 -r d8b6f0adaa79 test-data/bealign-out1.bam
Binary file test-data/bealign-out1.bam has changed