comparison miniprot.xml @ 5:6b20d051d0dc draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 810c6000c2d67e78764285c659c8082bbc573d71

4:00b22efdd100

<?xml version="1.0"?>
<tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>align a protein sequence against a genome with affine gap penalty, splicing and frameshift</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>

            -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

            <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>

                    <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"/>
                    <param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/>
                </section>
                <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
            </when>
            <when value="no">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
            <change_format>
                <when input="output_format" value="paf" format="paf"/>

            </conditional>
            <output name="output_alignment" ftype="gff3">
                <assert_contents>
                    <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">

            <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">

            <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>
        <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_no_cs" value="true"/>
                </section>

5:6b20d051d0dc

<?xml version="1.0"?>
<tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>align a protein sequence against a genome with affine gap penalty, splicing and frameshift</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>

            -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.ncbi_table) !=""
                -T '$adv.ncbi_table' 
            #end if
        #if str($adv.mapping.intron_size.mode) == 'manual'
            -G $adv.mapping.intron_size.max_intron      
        #elif str($adv.mapping.intron_size.mode) == 'auto'
            -I
        #end if

            <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>

                    <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"/>
                    <param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/>
                </section>
                <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
                <param argument="-T" name="ncbi_table" type="select" optional="true" label="Enter NCBI translation table">
                    <option value="1">1 Standard code</option>
                    <option value="2">2 Vertebrate mitochondrial</option>
                    <option value="3">3 Yeast mitochondrial</option>
                    <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option>
                    <option value="5">5 Invertebrate mitochondrial</option>
                    <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option>
                    <option value="9">9 Echinoderm and flatworm mitochondrial</option>
                    <option value="10">10 Euplotid nuclear</option>
                    <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option>
                    <option value="12">12 Alternative yeast nuclear</option>
                    <option value="13">13 Ascidian mitochondrial</option>
                    <option value="14">14 Alternative flatworm mitochondrial</option>
                    <option value="16">16 Chlorophycean mitochondrial</option>
                    <option value="21">21 Trematode Mitochondrial</option>
                    <option value="22">22 Scenedesmus obliquus Mitochondrial</option>
                    <option value="23">23 Thraustochytrium Mitochondrial</option>
                    <option value="24">24 Rhabdopleuridae Mitochondrial</option>
                    <option value="25">25 Candidate Division SR1 and Gracilibacteria</option>
                    <option value="26">26 Pachysolen tannophilus Nuclear</option>
                    <option value="27">27 Karyorelict Nuclear</option>
                    <option value="28">28 Condylostoma Nuclear</option>
                    <option value="29">29 Mesodinium nuclear</option>
                    <option value="30">30 Peritrich nuclear</option>
                    <option value="31">31 Blastocrithidia nuclear</option>
                    <option value="33">33 Cephalodiscidae mitochondrial</option>
                </param>
            </when>
            <when value="no">
            </when>
        </conditional>

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

            </conditional>
            <output name="output_alignment" ftype="gff3">
                <assert_contents>
                    <has_text text="tr|I6YGH7|I6YGH7_MYCTU" />
                    <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
                    <has_n_lines n="1647"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="db">

            <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="2196"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="db">

            <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="654"/>
                </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>
            <param name="ncbi_table" value="1"></param>
            <conditional name="adv">
                <param name="options" value="yes"></param>
                <section name="output">
                    <param name="output_no_cs" value="true"/>
                </section>