Mercurial > repos > iuc > bioext_bealign
diff bealign.xml @ 2:d8b6f0adaa79 draft
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
| author | iuc |
|---|---|
| date | Fri, 09 Jul 2021 15:19:05 +0000 |
| parents | f9b72a376ec9 |
| children | fb4975b507c6 |
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--- 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>