| Previous changeset 1:f9b72a376ec9 (2021-05-13) Next changeset 3:fb4975b507c6 (2021-08-20) |
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Commit message:
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0" |
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modified:
bealign.xml macros.xml test-data/bam2msa-out1.fa test-data/bealign-out1.bam |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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 ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ |
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| diff -r f9b72a376ec9 -r d8b6f0adaa79 test-data/bealign-out1.bam |
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| Binary file test-data/bealign-out1.bam has changed |