comparison miniprot.xml @ 2:d518cf04b55c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15

1:ce04c239454b

        miniprot
        -t \${GALAXY_SLOTS:-1}
        #if str($adv.options) == "yes"
            $adv.mapping.no_splicing
            -c $adv.mapping.max_kmer
            -G $adv.mapping.max_intron
            -n $adv.mapping.min_syncmers
            -m $adv.mapping.min_chain_score
            -l $adv.mapping.second_round_kmer_size
            -e $adv.mapping.max_extension
            -p $adv.mapping.score_ratio
            -N $adv.mapping.max_secondary_alignments
            -O $adv.alignment.gap_open
            -E $adv.alignment.gap_extension
            -J $adv.alignment.intron_open
            -C $adv.alignment.non_canonical_splice
            -F $adv.alignment.frameshift
            -B $adv.alignment.end_bonus
        #if str($adv.output.prefix) != 'MP'
            -P '$adv.output.prefix'
        #end if
            $adv.output.print_unmapped_proteins
            --outn=$adv.output.outputs_per_query
        #end if
        #if str($db.dbtype) == 'fasta'
            '$db.genomic_fasta'
            -k $db.kmer_size
            -s $db.submer_size
            -b $db.bits_per_block
        #else
            '$db.genomic_db'
        #end if
        #if str($output_format) == "gff"
            --gff
        #end if
        '$protein_fasta'
        >'$output_alignment'
    ]]></command>
    <inputs>
        <conditional name="db">
            <param name="dbtype" type="select" label="Database type" help="Build an index from FASTA or use a pre-indexed database">
                <option value="fasta" selected="true">FASTA</option>
                <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" />
                <param argument="-s" name="submer_size" type="integer" min="1" value="4" label="Submer size" help="Submer size (density: 1/(2*(kmer_size-submer_size)+1))" />
                <param argument="-b" name="bits_per_block" type="integer" min="1" value="8" label="Bits per block" />                
            </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" />
            </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" >
            <option value="gff" selected="true">GFF3</option>
            <option value="paf">PAF</option>
        </param>
        <conditional name="adv">
            <param name="options" type="select" label="Advanced options">
                <option value="yes">Show</option>
                <option value="no" selected="true">Hide</option>
            </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="50000" label="Max k-mer occurences" />
                    <param argument="-G" name="max_intron" type="integer" min="0" value="200000" label="Max intron size" />
                    <!-- the -w option is mentioned in the help text but apparently not implmented: https://github.com/lh3/miniprot/issues/12 -->
                    <!-- <param argument="-w" name="log_gap_penalty_weight" type="float" value="0.75" label="Log gap penalty weight" /> -->
                    <param argument="-n" name="min_syncmers" type="integer" min="1" value="5" 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="50" label="Max secondary alignments to consider" />
                </section>
                <section name="alignment" title="Alignment">
                    <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="31" label="Intron open penalty" />
                    <param argument="-C" name="non_canonical_splice" type="integer" min="0" value="11" label="Penalty for non-canonical splicing" />
                    <param argument="-F" name="frameshift" type="integer" min="0" value="17" label="Frameshift penalty" />
                    <param argument="-B" name="end_bonus" type="integer" min="0" value="5" label="End bonus" />
                </section>
                <section name="output" title="Output">
                    <param argument="-P" name="prefix" type="text" label="Prefix for IDs in GFF3 output" value="MP">
                        <sanitizer invalid_char="">
                            <valid initial="string.ascii_letters,string.digits">

                            </valid>
                        </sanitizer>
                    </param>
                    <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" />
                </section>
                <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size" />
            </when>
            <when value="no">
            </when>

    </inputs>
    <outputs>
        <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
            <change_format>
                <when input="output_format" value="paf" format="paf" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">

                <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
            </conditional>
            <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
            <output name="output_alignment" ftype="gff3">
                <assert_contents>
                    <has_text text="ID=MP000001;Identity=1.0000;Positive=1.0000;Target=tr|O06302|O06302_MYCTU 1 126" />
                    <has_text text="ID=MP000359;Identity=0.9811;Positive=1.0000;Target=tr|V5QPR5|V5QPR5_MYCTU 1 53" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="db">

                <assert_contents>
                    <has_text text="tr|O06302|O06302_MYCTU" />
                    <has_text text="cs:Z::29*agcG:3*gtgA:5*ccgA:9*accS:1*gccV:4*cagL:1*gtcS:3*gtcA*gtcI*accA*gccG:8*gccS:2*ggtA:5*gccI*agcG:1*ctgA:4*gccV:5*gggL:1*gtgS:2" />
                </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" />
            </conditional>

                <assert_contents>
                    <has_text text="##gff-version 3" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        miniprot_  rapidly aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
        It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.

        For details of the algorithm and some insight into how parameters can be tuned see this overview_.

        .. _miniprot: https://github.com/lh3/miniprot
        .. _overview: https://github.com/lh3/miniprot#algorithm-overview
    ]]></help>
    <citations>
        <citation type="bibtex"><![CDATA[
            @misc{Li2022,
                author = {Li, Heng},
                title = {miniprot},
                year = {2022},
                publisher = {GitHub},
                journal = {GitHub repository},
                howpublished = {\url{https://github.com/lh3/miniprot}},
                commit = {b442b7a6b60dbd15f460ea9af75fa0b7293d4a8c}
              }            
        ]]></citation>
    </citations>    
</tool>

2:d518cf04b55c

        miniprot
        -t \${GALAXY_SLOTS:-1}
        #if str($adv.options) == "yes"
            $adv.mapping.no_splicing
            -c $adv.mapping.max_kmer
            -n $adv.mapping.min_syncmers
            -m $adv.mapping.min_chain_score
            -l $adv.mapping.second_round_kmer_size
            -e $adv.mapping.max_extension
            -p $adv.mapping.score_ratio
            -N $adv.mapping.max_secondary_alignments
            -w $adv.mapping.log_gap_penalty_weight
            -O $adv.alignment.gap_open
            -E $adv.alignment.gap_extension
            -J $adv.alignment.intron_open
            -C $adv.alignment.non_canonical_splice
            -F $adv.alignment.frameshift
            -B $adv.alignment.end_bonus
            -j $adv.alignment.splice_model 
        #if str($adv.mapping.intron_size.mode) == 'manual'
            -G $adv.mapping.intron_size.max_intron      
        #elif str($adv.mapping.intron_size.mode) == 'auto'
             -I
        #end if
    
        #if str($adv.output.prefix) != 'MP'
            -P '$adv.output.prefix'
        #end if
            $adv.output.print_unmapped_proteins
            --outn=$adv.output.outputs_per_query
            --outc=$adv.output.output_fraction_query
            --outs=$adv.output.output_score_least
            $adv.output.output_residue_alignment
        #end if
        #if str($db.dbtype) == 'fasta'
            '$db.genomic_fasta'
            -k $db.kmer_size
            -b $db.bits_per_block  
            -M $db.modimisers
            -L $db.min_ORF
        #else
            '$db.genomic_db'
        #end if
        #if str($output_format) == "gff"
            --gff
        #else if str($output_format) == "gtf"
            --gtf
        #end if
        '$protein_fasta' > '$output_alignment'
    ]]></command>
    <inputs>
        <conditional name="db">
            <param name="dbtype" type="select" label="Database type" help="Build an index from FASTA or use a pre-indexed database">
                <option value="fasta" selected="true">FASTA</option>
                <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 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" />           
            </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" />
            </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" >
            <option value="gff" selected="true">GFF3</option>
            <option value="paf">PAF</option>
            <option value="gtf">GTF</option>
        </param>
        <conditional name="adv">
            <param name="options" type="select" label="Advanced options">
                <option value="yes">Show</option>
                <option value="no" selected="true">Hide</option>
            </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" />
                    <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" />
                        </when> 
                        <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="-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" >
                        <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>
                    </param>
                </section>
                <section name="output" title="Output">
                    <param argument="-P" name="prefix" type="text" label="Prefix for IDs in GFF3 output" value="MP">
                        <sanitizer invalid_char="">
                            <valid initial="string.ascii_letters,string.digits">

                            </valid>
                        </sanitizer>
                    </param>
                    <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" />
                </section>
                <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size" />
            </when>
            <when value="no">
            </when>

    </inputs>
    <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="gtf" format="gtf"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">

                <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
            </conditional>
            <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" /> 
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="db">

                <assert_contents>
                    <has_text text="tr|O06302|O06302_MYCTU" />
                    <has_text text="cs:Z::29*agcG:3*gtgA:5*ccgA:9*accS:1*gccV:4*cagL:1*gtcS:3*gtcA*gtcI*accA*gccG:8*gccS:2*ggtA:5*gccI*agcG:1*ctgA:4*gccV:5*gggL:1*gtgS:2" />
                </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" />
            </conditional>

                <assert_contents>
                    <has_text text="##gff-version 3" />
                </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>
                <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"' />
                </assert_contents>
            </output>
        </test>


    </tests>
    <help><![CDATA[
        miniprot_  rapidly aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
        It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.

        For details of the algorithm and some insight into how parameters can be tuned see this overview_.

        .. _miniprot: https://github.com/lh3/miniprot
        .. _overview: https://github.com/lh3/miniprot#algorithm-overview
    ]]></help> 
    <expand macro="citation"></expand>
</tool>