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Miniprot Update version v0.10 to v0.12 #5317

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merged 16 commits into from
Jul 13, 2023
Merged

Miniprot Update version v0.10 to v0.12 #5317

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86f5c02
Update version
rlibouba May 22, 2023
18b4eec
Add test for the new param
rlibouba May 23, 2023
7ca6bb1
Update tools/miniprot/miniprot.xml
rlibouba May 23, 2023
77a7724
Missing value
rlibouba May 23, 2023
f21026d
Modification param
rlibouba May 23, 2023
1c2f39c
Modification test for new param
rlibouba May 23, 2023
66c4fd0
Test
rlibouba May 23, 2023
7a855d6
Add new test
rlibouba May 24, 2023
ee4fd69
Tests
rlibouba May 24, 2023
389696b
New test
rlibouba May 24, 2023
7ffc3ab
Comment added for trans parameter
rlibouba Jun 14, 2023
61108f6
Modification input section - trans param
rlibouba Jun 14, 2023
c93be51
modifications
rlibouba Jun 15, 2023
71f5322
Modications tests
rlibouba Jun 21, 2023
032697b
Add new version 0.12 and news options
rlibouba Jul 4, 2023
2af23d9
style fixes
bgruening Jul 4, 2023
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2 changes: 1 addition & 1 deletion tools/miniprot/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">0.10</token>
<token name="@TOOL_VERSION@">0.11</token>
<xml name="citation">
<citations>
<citation type="doi">10.1093/bioinformatics/btad014</citation>
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21 changes: 21 additions & 0 deletions tools/miniprot/miniprot.xml
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Expand Up @@ -40,6 +40,7 @@
--outn=$adv.output.outputs_per_query
--outc=$adv.output.output_fraction_query
--outs=$adv.output.output_score_least
$adv.output.output_translated_protein
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$adv.output.output_residue_alignment
#end if
#if str($db.dbtype) == 'fasta'
Expand Down Expand Up @@ -137,6 +138,7 @@
<param argument="--outs" name="output_score_least" type="float" min="0" max="1" value="0.99"
label="For each protein, only output alignments with a score higher than 'best_score' multiplied by this value"/>
<param argument="--outc" name="output_fraction_query" type="float" value="0.1" label="Output if at least this fraction of query is aligned" />
<param argument="--trans" name="output_translated_protein" type="boolean" truevalue="--trans" falsevalue="" checked="false" label="Output translated protein sequences" help="Skipping frameshift" />
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</section>
<param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size" />
</when>
Expand Down Expand Up @@ -217,6 +219,25 @@
</output>
</test>

<test expect_num_outputs="1">
<conditional name="db">
<param name="dbtype" value="fasta"></param>
<param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
</conditional>
<param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
<param name="output_format" value="gtf"></param>
<conditional name="adv">
<param name="options" value="yes"></param>
<param name="second_round_kmer_size" value="32"></param>
<param name="output_translated_protein" />
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</conditional>
<output name="output_alignment" ftype="gtf">
<assert_contents>
<has_text text="tr|I6YGH7|I6YGH7_MYCTU" />
<has_text text="tr|V5QPR5|V5QPR5_MYCTU"/>
</assert_contents>
</output>
</test>

</tests>
<help><![CDATA[
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