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annotate miniprot.xml @ 2:d518cf04b55c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
author iuc
date Thu, 06 Apr 2023 09:20:48 +0000
parents ce04c239454b
children 52bdc302299b
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ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
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1 <?xml version="1.0"?>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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2 <tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy0" profile="21.05">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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3 <description>align a protein sequence against a genome with affine gap penalty, splicing and frameshift</description>
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4 <macros>
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5 <import>macros.xml</import>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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6 </macros>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">miniprot</requirement>
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9 </requirements>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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10 <command detect_errors="exit_code"><![CDATA[
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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11 miniprot
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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12 -t \${GALAXY_SLOTS:-1}
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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13 #if str($adv.options) == "yes"
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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14 $adv.mapping.no_splicing
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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15 -c $adv.mapping.max_kmer
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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16 -n $adv.mapping.min_syncmers
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17 -m $adv.mapping.min_chain_score
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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18 -l $adv.mapping.second_round_kmer_size
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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19 -e $adv.mapping.max_extension
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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20 -p $adv.mapping.score_ratio
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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21 -N $adv.mapping.max_secondary_alignments
2
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22 -w $adv.mapping.log_gap_penalty_weight
0
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23 -O $adv.alignment.gap_open
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24 -E $adv.alignment.gap_extension
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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25 -J $adv.alignment.intron_open
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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26 -C $adv.alignment.non_canonical_splice
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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27 -F $adv.alignment.frameshift
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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28 -B $adv.alignment.end_bonus
2
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29 -j $adv.alignment.splice_model
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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30 #if str($adv.mapping.intron_size.mode) == 'manual'
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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31 -G $adv.mapping.intron_size.max_intron
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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32 #elif str($adv.mapping.intron_size.mode) == 'auto'
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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33 -I
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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34 #end if
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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35
1
ce04c239454b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit fbe24c1f66f23448d48a61c84a93cb73e0dbc779
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36 #if str($adv.output.prefix) != 'MP'
ce04c239454b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit fbe24c1f66f23448d48a61c84a93cb73e0dbc779
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37 -P '$adv.output.prefix'
ce04c239454b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit fbe24c1f66f23448d48a61c84a93cb73e0dbc779
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38 #end if
ce04c239454b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit fbe24c1f66f23448d48a61c84a93cb73e0dbc779
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39 $adv.output.print_unmapped_proteins
ce04c239454b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit fbe24c1f66f23448d48a61c84a93cb73e0dbc779
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40 --outn=$adv.output.outputs_per_query
2
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41 --outc=$adv.output.output_fraction_query
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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42 --outs=$adv.output.output_score_least
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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43 $adv.output.output_residue_alignment
0
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44 #end if
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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45 #if str($db.dbtype) == 'fasta'
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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46 '$db.genomic_fasta'
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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47 -k $db.kmer_size
2
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48 -b $db.bits_per_block
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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49 -M $db.modimisers
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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50 -L $db.min_ORF
0
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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51 #else
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52 '$db.genomic_db'
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53 #end if
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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54 #if str($output_format) == "gff"
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55 --gff
2
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56 #else if str($output_format) == "gtf"
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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57 --gtf
0
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58 #end if
2
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59 '$protein_fasta' > '$output_alignment'
0
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60 ]]></command>
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61 <inputs>
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62 <conditional name="db">
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63 <param name="dbtype" type="select" label="Database type" help="Build an index from FASTA or use a pre-indexed database">
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64 <option value="fasta" selected="true">FASTA</option>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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65 <option value="preindexed">Pre-indexed</option>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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66 </param>
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67 <when value="fasta">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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68 <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" />
2
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69 <param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing" />
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70 <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" />
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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71 <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" />
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
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72 <param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index" />
0
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73 </when>
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74 <when value="preindexed">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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75 <!-- refine the datatype here once Miniprot index data type is in Galaxy -->
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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76 <param name="genomic_db" type="data" format="binary" label="Pre-indexed genomic database" help="A pre-indexed database built by miniprot" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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77 </when>
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78 </conditional>
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79 <param name="protein_fasta" type="data" format="fasta,fasta.gz" label="Protein sequence (FASTA)" help="Protein sequences to be aligned in FASTA format" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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80 <param name="output_format" type="select" label="Output format" >
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81 <option value="gff" selected="true">GFF3</option>
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82 <option value="paf">PAF</option>
2
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83 <option value="gtf">GTF</option>
0
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84 </param>
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85 <conditional name="adv">
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86 <param name="options" type="select" label="Advanced options">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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87 <option value="yes">Show</option>
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88 <option value="no" selected="true">Hide</option>
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89 </param>
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90 <when value="yes">
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91 <section name="mapping" title="Mapping">
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92 <param argument="-S" name="no_splicing" type="boolean" truevalue="-S" falsevalue="" checked="false" label="No splicing" help="No splicing (apply -G1000 -J1000 -e1000)" />
2
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93 <param argument="-c" name="max_kmer" type="integer" min="1" value="20000" label="Max k-mer occurences" />
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94 <param argument="-w" name="log_gap_penalty_weight" type="float" min="0" max="1" value="0.75" label="Log gap penalty weight" />
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95 <param argument="-n" name="min_syncmers" type="integer" min="1" value="3" label="Minimum number of syncmers in a chain" />
0
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96 <param argument="-m" name="min_chain_score" type="integer" min="0" value="0" label="Minimum chaining score" />
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97 <param argument="-l" name="second_round_kmer_size" type="integer" min="1" value="5" label="K-mer size for second round of chaining" />
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98 <param argument="-e" name="max_extension" type="integer" min="0" value="10000" label="Max extension for second round of chaining" />
1
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99 <param argument="-p" name="score_ratio" type="float" min="0" max="1" value="0.7" label="Minimum secondary-to-primary score ratio" />
2
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100 <param argument="-N" name="max_secondary_alignments" type="integer" min="0" value="30" label="Max secondary alignments to consider" />
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101 <conditional name="intron_size">
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102 <param name="mode" type="select" label="Maximum intron size">
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103 <option value="manual" selected="true">Manual</option>
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104 <option value="auto">Auto (3.6*sqrt)</option>
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105 </param>
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106 <when value="manual">
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107 <param argument="-G" name="max_intron" type="integer" min="0" value="200000" label="Maximum intron size" />
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108 </when>
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109 <when value="auto" />
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110 </conditional>
0
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111 </section>
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112 <section name="alignment" title="Alignment">
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113 <param argument="-O" name="gap_open" type="integer" min="0" value="11" label="Gap open penalty" />
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114 <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" />
2
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115 <param argument="-J" name="intron_open" type="integer" min="0" value="29" label="Intron open penalty" />
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116 <param argument="-C" name="non_canonical_splice" type="float" value="1" label="Weight of splice penalty; 0 to ignore splice signals" />
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117 <param argument="-F" name="frameshift" type="integer" min="0" value="23" label="Frameshift penalty" />
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118 <param argument="-B" name="end_bonus" type="integer" min="0" value="5" label="Bonus score for alignment reaching query ends" />
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119 <param argument="-j" name="splice_model" type="select" label="Splicing model for the target genome" help="2=mammal, 1=general, 0=none" >
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120 <option value="O" >None: No splicing model (0)</option>
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121 <option value="1" selected="true">General: Optimal splicing sequence: '|GTR...YAG|' (1)</option>
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122 <option value="2">Mammal: Optimal splicing sequence: 'G|GTR...YYYNYAG|' (2)</option>
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123 </param>
0
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124 </section>
1
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125 <section name="output" title="Output">
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126 <param argument="-P" name="prefix" type="text" label="Prefix for IDs in GFF3 output" value="MP">
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127 <sanitizer invalid_char="">
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128 <valid initial="string.ascii_letters,string.digits">
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129 <add value="_" />
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130 <add value="-" />
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131 </valid>
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132 </sanitizer>
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133 </param>
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134 <param argument="-u" name="print_unmapped_proteins" type="boolean" truevalue="-u" falsevalue="" label="Print unmapped proteins" checked="false" />
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135 <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" />
2
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136 <param argument="--aln" name="output_residue_alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Output residue alignment" help="Only for GFF output" />
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137 <param argument="--outs" name="output_score_least" type="float" min="0" max="1" value="0.99"
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138 label="For each protein, only output alignments with a score higher than 'best_score' multiplied by this value"/>
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139 <param argument="--outc" name="output_fraction_query" type="float" value="0.1" label="Output if at least this fraction of query is aligned" />
1
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140 </section>
0
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141 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size" />
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142 </when>
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143 <when value="no">
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144 </when>
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145 </conditional>
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146 </inputs>
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147 <outputs>
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148 <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
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149 <change_format>
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150 <when input="output_format" value="paf" format="paf" />
2
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151 <when input="output_format" value="gtf" format="gtf"/>
0
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152 </change_format>
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153 </data>
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154 </outputs>
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155 <tests>
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156 <test expect_num_outputs="1">
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157 <conditional name="db">
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158 <param name="dbtype" value="fasta" />
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159 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
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160 </conditional>
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161 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
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162 <output name="output_alignment" ftype="gff3">
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163 <assert_contents>
2
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164 <has_text text="ID=MP000001;Rank=1;Identity=0.3420;Positive=0.5104;Target=tr|I6YGH7|I6YGH7_MYCTU 1 375" />
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165 <has_text text="ID=MP000066;Rank=1;Identity=0.3613;Positive=0.5178;Target=sp|P9WQE5|PPSB_MYCTU 1 1214" />
0
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166 </assert_contents>
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167 </output>
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168 </test>
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169 <test expect_num_outputs="1">
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170 <conditional name="db">
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171 <param name="dbtype" value="fasta" />
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172 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
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173 </conditional>
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174 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
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175 <param name="output_format" value="paf" />
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176 <output name="output_alignment" ftype="paf">
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177 <assert_contents>
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178 <has_text text="tr|O06302|O06302_MYCTU" />
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179 <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" />
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180 </assert_contents>
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181 </output>
2
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182 </test>
0
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183 <test expect_num_outputs="1">
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184 <conditional name="db">
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185 <param name="dbtype" value="fasta" />
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186 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
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187 </conditional>
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188 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
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189 <param name="output_format" value="gff" />
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190 <conditional name="adv">
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191 <param name="options" value="yes" />
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192 <param name="second_round_kmer_size" value="32" />
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193 </conditional>
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194 <output name="output_alignment" ftype="gff3">
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195 <assert_contents>
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196 <has_text text="##gff-version 3" />
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197 </assert_contents>
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198 </output>
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199 </test>
2
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200
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201 <test expect_num_outputs="1">
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202 <conditional name="db">
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203 <param name="dbtype" value="fasta"></param>
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204 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
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205 </conditional>
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206 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
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207 <param name="output_format" value="gtf"></param>
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208 <conditional name="adv">
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209 <param name="options" value="yes"></param>
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210 <param name="second_round_kmer_size" value="32"></param>
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211 </conditional>
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212 <output name="output_alignment" ftype="gtf">
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213 <assert_contents>
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214 <has_text text="NC_000962.3" />
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215 <has_text text='transcript_id "MPT000004"; gene_id "MPG000004"' />
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216 </assert_contents>
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217 </output>
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218 </test>
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219
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220
0
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221 </tests>
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222 <help><![CDATA[
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223 miniprot_ rapidly aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
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224 It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
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225
1
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226 While an index of the genome to be mapped to can be built "on the fly", the Miniprot index tool can pre-index a genome
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227 and will result in faster performance if the genome index is reused multiple times.
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228
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229 For details of the algorithm and some insight into how parameters can be tuned see this overview_.
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230
0
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231 .. _miniprot: https://github.com/lh3/miniprot
1
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232 .. _overview: https://github.com/lh3/miniprot#algorithm-overview
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233 ]]></help>
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234 <expand macro="citation"></expand>
0
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235 </tool>