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annotate tests.xml @ 0:a14d5c1e1fc4 draft default tip

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planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
author iuc
date Sun, 09 Nov 2025 10:56:21 +0000
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a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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1 <macros>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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2 <xml name="tests">
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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3 <tests>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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4 <test expect_num_outputs="1">
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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5 <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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6 <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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7 <param name="output_format" value="paml" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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8 <output name="output_file" file="outputs/expected_paml.paml" ftype="phylip" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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9 </test>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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10 <test expect_num_outputs="1">
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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11 <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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12 <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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13 <param name="output_format" value="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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14 <output name="output_file" file="outputs/expected_clustal.aln" ftype="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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15 </test>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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16 <test expect_num_outputs="1">
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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17 <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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18 <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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19 <param name="output_format" value="fasta" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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20 <param name="remove_gaps" value="true" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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21 <output name="output_file" file="outputs/expected_nogap.fasta" ftype="fasta" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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22 </test>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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23 <test expect_num_outputs="1">
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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24 <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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25 <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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26 <param name="output_format" value="codon" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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27 <output name="output_file" file="outputs/expected_codon.txt" ftype="txt" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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28 </test>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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29 <test expect_num_outputs="1">
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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30 <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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31 <param name="nucleotide_fastas" value="inputs/test_bc070280.fasta,inputs/test_pseudogene.fasta" ftype="fasta" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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32 <param name="output_format" value="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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33 <output name="output_file" file="outputs/expected_clustal_multi.aln" ftype="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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34 </test>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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35 <test expect_num_outputs="2">
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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36 <param name="protein_alignment" value="inputs/test.aln" ftype="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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37 <param name="nucleotide_fastas" value="inputs/test.nuc" ftype="fasta" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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38 <param name="output_format" value="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
iuc
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39 <param name="show_only_blocks" value="true" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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40 <param name="remove_mismatches" value="true" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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41 <param name="genetic_code" value="2" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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42 <param name="html_output" value="true" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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43 <param name="suppress_stderr" value="true" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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44 <output name="output_file" file="outputs/expected_block_nomismatch.aln" ftype="clustal" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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45 <output name="html_output_file" file="outputs/expected_html.html" ftype="html" />
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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46 </test>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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47 </tests>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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48 </xml>
a14d5c1e1fc4 planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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49 </macros>