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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
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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
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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>
Expand Down
149 changes: 108 additions & 41 deletions tools/miniprot/miniprot.xml
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Expand Up @@ -30,7 +30,7 @@
#if str($adv.mapping.intron_size.mode) == 'manual'
-G $adv.mapping.intron_size.max_intron
#elif str($adv.mapping.intron_size.mode) == 'auto'
-I
-I
#end if

#if str($adv.output.prefix) != 'MP'
Expand All @@ -40,6 +40,7 @@
--outn=$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 All @@ -65,19 +66,19 @@
<option value="preindexed">Pre-indexed</option>
</param>
<when value="fasta">
<param name="genomic_fasta" type="data" format="fasta,fasta.gz" label="Genomic sequence (FASTA)" help="Genomic contigs / scaffolds to be aligned against in FASTA format" />
<param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing" />
<param name="genomic_fasta" type="data" format="fasta,fasta.gz" label="Genomic sequence (FASTA)" help="Genomic contigs / scaffolds to be aligned against in FASTA format"/>
<param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing"/>
<param argument="-b" name="bits_per_block" type="integer" min="1" value="8" label="Number of bits per bin" help="Miniprot splits the genome into non-overlapping bins of 2^8 bp in size" />
<param argument="-M" name="modimisers" type="integer" value="1" label="Sample k-mers at a rate 1/2**INT" help="Increasing this option reduces peak memory but decreases sensitivity" />
<param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index" />
<param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index"/>
</when>
<when value="preindexed">
<!-- refine the datatype here once Miniprot index data type is in Galaxy -->
<param name="genomic_db" type="data" format="binary" label="Pre-indexed genomic database" help="A pre-indexed database built by miniprot" />
<param name="genomic_db" type="data" format="binary" label="Pre-indexed genomic database" help="A pre-indexed database built by miniprot"/>
</when>
</conditional>
<param name="protein_fasta" type="data" format="fasta,fasta.gz" label="Protein sequence (FASTA)" help="Protein sequences to be aligned in FASTA format" />
<param name="output_format" type="select" label="Output format" >
<param name="protein_fasta" type="data" format="fasta,fasta.gz" label="Protein sequence (FASTA)" help="Protein sequences to be aligned in FASTA format"/>
<param name="output_format" type="select" label="Output format">
<option value="gff" selected="true">GFF3</option>
<option value="paf">PAF</option>
<option value="gtf">GTF</option>
Expand All @@ -89,34 +90,34 @@
</param>
<when value="yes">
<section name="mapping" title="Mapping">
<param argument="-S" name="no_splicing" type="boolean" truevalue="-S" falsevalue="" checked="false" label="No splicing" help="No splicing (apply -G1000 -J1000 -e1000)" />
<param argument="-c" name="max_kmer" type="integer" min="1" value="20000" label="Max k-mer occurences" />
<param argument="-w" name="log_gap_penalty_weight" type="float" min="0" max="1" value="0.75" label="Log gap penalty weight" />
<param argument="-n" name="min_syncmers" type="integer" min="1" value="3" label="Minimum number of syncmers in a chain" />
<param argument="-m" name="min_chain_score" type="integer" min="0" value="0" label="Minimum chaining score" />
<param argument="-l" name="second_round_kmer_size" type="integer" min="1" value="5" label="K-mer size for second round of chaining" />
<param argument="-e" name="max_extension" type="integer" min="0" value="10000" label="Max extension for second round of chaining" />
<param argument="-p" name="score_ratio" type="float" min="0" max="1" value="0.7" label="Minimum secondary-to-primary score ratio" />
<param argument="-N" name="max_secondary_alignments" type="integer" min="0" value="30" label="Max secondary alignments to consider" />
<param argument="-S" name="no_splicing" type="boolean" truevalue="-S" falsevalue="" checked="false" label="No splicing" help="No splicing (apply -G1000 -J1000 -e1000)"/>
<param argument="-c" name="max_kmer" type="integer" min="1" value="20000" label="Max k-mer occurences"/>
<param argument="-w" name="log_gap_penalty_weight" type="float" min="0" max="1" value="0.75" label="Log gap penalty weight"/>
<param argument="-n" name="min_syncmers" type="integer" min="1" value="3" label="Minimum number of syncmers in a chain"/>
<param argument="-m" name="min_chain_score" type="integer" min="0" value="0" label="Minimum chaining score"/>
<param argument="-l" name="second_round_kmer_size" type="integer" min="1" value="5" label="K-mer size for second round of chaining"/>
<param argument="-e" name="max_extension" type="integer" min="0" value="10000" label="Max extension for second round of chaining"/>
<param argument="-p" name="score_ratio" type="float" min="0" max="1" value="0.7" label="Minimum secondary-to-primary score ratio"/>
<param argument="-N" name="max_secondary_alignments" type="integer" min="0" value="30" label="Max secondary alignments to consider"/>
<conditional name="intron_size">
<param name="mode" type="select" label="Maximum intron size">
<option value="manual" selected="true">Manual</option>
<option value="auto">Auto (3.6*sqrt)</option>
</param>
<when value="manual">
<param argument="-G" name="max_intron" type="integer" min="0" value="200000" label="Maximum intron size" />
<param argument="-G" name="max_intron" type="integer" min="0" value="200000" label="Maximum intron size"/>
</when>
<when value="auto" />
<when value="auto"/>
</conditional>
</section>
<section name="alignment" title="Alignment">
<param argument="-O" name="gap_open" type="integer" min="0" value="11" label="Gap open penalty" />
<param argument="-O" name="gap_open" type="integer" min="0" value="11" label="Gap open penalty"/>
<param argument="-E" name="gap_extension" type="integer" min="0" value="1" label="Gap extension penalty" help="A k-long gap costs open_penalty+k*extension_penalty" />
<param argument="-J" name="intron_open" type="integer" min="0" value="29" label="Intron open penalty" />
<param argument="-C" name="non_canonical_splice" type="float" value="1" label="Weight of splice penalty; 0 to ignore splice signals" />
<param argument="-F" name="frameshift" type="integer" min="0" value="23" label="Frameshift penalty" />
<param argument="-B" name="end_bonus" type="integer" min="0" value="5" label="Bonus score for alignment reaching query ends" />
<param argument="-j" name="splice_model" type="select" label="Splicing model for the target genome" help="2=mammal, 1=general, 0=none" >
<param argument="-J" name="intron_open" type="integer" min="0" value="29" label="Intron open penalty"/>
<param argument="-C" name="non_canonical_splice" type="float" value="1" label="Weight of splice penalty; 0 to ignore splice signals"/>
<param argument="-F" name="frameshift" type="integer" min="0" value="23" label="Frameshift penalty"/>
<param argument="-B" name="end_bonus" type="integer" min="0" value="5" label="Bonus score for alignment reaching query ends"/>
<param argument="-j" name="splice_model" type="select" label="Splicing model for the target genome" help="2=mammal, 1=general, 0=none">
<option value="O" >None: No splicing model (0)</option>
<option value="1" selected="true">General: Optimal splicing sequence: '|GTR...YAG|' (1)</option>
<option value="2">Mammal: Optimal splicing sequence: 'G|GTR...YYYNYAG|' (2)</option>
Expand All @@ -131,14 +132,16 @@
</valid>
</sanitizer>
</param>
<param argument="-u" name="print_unmapped_proteins" type="boolean" truevalue="-u" falsevalue="" label="Print unmapped proteins" checked="false" />
<param argument="-u" name="print_unmapped_proteins" type="boolean" truevalue="-u" falsevalue="" label="Print unmapped proteins" checked="false"/>
<param argument="--outn" name="outputs_per_query" type="integer" min="0" value="100" label="Outputs per query" help="The number of outputs will be the minimum of this and the max secondary alignments option" />
<param argument="--aln" name="output_residue_alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Output residue alignment" help="Only for GFF output" />
<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="--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" /> -->
<!-- Warning: there is a bug with the -trans parameter for gtf output. A release is underway to correct this. -->
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</section>
<param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size" />
<param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
</when>
<when value="no">
</when>
Expand All @@ -147,7 +150,7 @@
<outputs>
<data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
<change_format>
<when input="output_format" value="paf" format="paf" />
<when input="output_format" value="paf" format="paf"/>
<when input="output_format" value="gtf" format="gtf"/>
</change_format>
</data>
Expand All @@ -156,22 +159,22 @@
<test expect_num_outputs="1">
<conditional name="db">
<param name="dbtype" value="fasta" />
<param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
<param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"/>
</conditional>
<param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
<param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"/>
<output name="output_alignment" ftype="gff3">
<assert_contents>
<has_text text="ID=MP000001;Rank=1;Identity=0.3420;Positive=0.5104;Target=tr|I6YGH7|I6YGH7_MYCTU 1 375" />
<has_text text="ID=MP000066;Rank=1;Identity=0.3613;Positive=0.5178;Target=sp|P9WQE5|PPSB_MYCTU 1 1214" />
<has_text text="ID=MP000001;Rank=1;Identity=0.3420;Positive=0.5104;Target=tr|I6YGH7|I6YGH7_MYCTU 1 375"/>
<has_text text="ID=MP000066;Rank=1;Identity=0.3613;Positive=0.5178;Target=sp|P9WQE5|PPSB_MYCTU 1 1214"/>
</assert_contents>
</output>
</test>
<test expect_num_outputs="1">
<conditional name="db">
<param name="dbtype" value="fasta" />
<param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
<param name="dbtype" value="fasta"/>
<param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"/>
</conditional>
<param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
<param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"/>
<param name="output_format" value="paf" />
<output name="output_alignment" ftype="paf">
<assert_contents>
Expand All @@ -183,13 +186,13 @@
<test expect_num_outputs="1">
<conditional name="db">
<param name="dbtype" value="fasta" />
<param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
<param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"/>
</conditional>
<param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
<param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"/>
<param name="output_format" value="gff" />
<conditional name="adv">
<param name="options" value="yes" />
<param name="second_round_kmer_size" value="32" />
<param name="second_round_kmer_size" value="32"/>
</conditional>
<output name="output_alignment" ftype="gff3">
<assert_contents>
Expand All @@ -207,16 +210,80 @@
<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>
</conditional>
<output name="output_alignment" ftype="gtf">
<assert_contents>
<has_text text="NC_000962.3" />
<has_text text='transcript_id "MPT000004"; gene_id "MPG000004"' />
<has_text text='transcript_id "MPT000004"; gene_id "MPG000004"'/>
</assert_contents>
</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="gff"></param>
<conditional name="adv">
<param name="options" value="yes"/>
<section name="output">
<param name="output_translated_protein" value="true"/>
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</section>
</conditional>
<output name="output_alignment" ftype="gff3">
<assert_contents>
<has_text text="##gff-version 3"/>
<has_text text="tr|I6YGH7|I6YGH7_MYCTU" />
<has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
<has_n_lines n="1633"/>
</assert_contents>
</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>
<section name="output">
<param name="output_translated_protein" value="true"/>
</section> </conditional>
<output name="output_alignment" ftype="gtf">
<assert_contents>
<has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
<has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
<has_text text="NC_000962.3"/>
<has_n_lines n="2172"/>
</assert_contents>
</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="paf"></param>
<conditional name="adv">
<param name="options" value="yes"></param>
<section name="output">
<param name="output_translated_protein" value="true"/>
</section> </conditional>
<output name="output_alignment" ftype="paf">
<assert_contents>
<has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
<has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
<has_text text="sp|O05779|FTSE_MYCTU"/>
<has_n_lines n="650"/>
</assert_contents>
</output>
</test>

</tests>
<help><![CDATA[
Expand All @@ -232,4 +299,4 @@
.. _overview: https://github.com/lh3/miniprot#algorithm-overview
]]></help>
<expand macro="citation"></expand>
</tool>
</tool>
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