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annotate miniprot.xml @ 0:ef712a5e9834 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
author iuc
date Mon, 19 Sep 2022 12:30:10 +0000
parents
children ce04c239454b
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0
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
iuc
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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
iuc
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3 <description>align a protein sequence against a genome with affine gap penalty, splicing and frameshift</description>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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4 <macros>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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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>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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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 -G $adv.mapping.max_intron
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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17 -n $adv.mapping.min_syncmers
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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18 -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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19 -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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20 -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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21 -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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22 -N $adv.mapping.max_secondary_alignments
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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23 -O $adv.alignment.gap_open
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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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 $adv.alignment.end_bonus
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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29 #end if
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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30 #if str($db.dbtype) == 'fasta'
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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31 '$db.genomic_fasta'
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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32 -k $db.kmer_size
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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33 -s $db.submer_size
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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34 -b $db.bits_per_block
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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35 #else
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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36 '$db.genomic_db'
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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37 #end if
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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38 #if str($output_format) == "gff"
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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39 --gff
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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40 #end if
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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41 '$protein_fasta'
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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42 >'$output_alignment'
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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43 ]]></command>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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44 <inputs>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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45 <conditional name="db">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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46 <param name="dbtype" type="select" label="Database type" help="Build an index from FASTA or use a pre-indexed database">
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47 <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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48 <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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49 </param>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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50 <when value="fasta">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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51 <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" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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52 <param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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53 <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))" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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54 <param argument="-b" name="bits_per_block" type="integer" min="1" value="8" label="Bits per block" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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55 </when>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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56 <when value="preindexed">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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57 <!-- 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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58 <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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59 </when>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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60 </conditional>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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61 <param name="protein_fasta" type="data" format="fasta,fasta.gz" label="Protein sequence (FASTA)" help="Protein sequences to be aligned in FASTA format" />
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62 <param name="output_format" type="select" label="Output format" >
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63 <option value="gff" selected="true">GFF3</option>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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64 <option value="paf">PAF</option>
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65 </param>
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66 <conditional name="adv">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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67 <param name="options" type="select" label="Advanced options">
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68 <option value="yes">Show</option>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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69 <option value="no" selected="true">Hide</option>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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70 </param>
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71 <when value="yes">
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72 <section name="mapping" title="Mapping">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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73 <param argument="-S" name="no_splicing" type="boolean" truevalue="-S" falsevalue="" checked="false" label="No splicing" help="No splicing (apply -G1000 -J1000 -e1000)" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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74 <param argument="-c" name="max_kmer" type="integer" min="1" value="50000" label="Max k-mer occurences" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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75 <param argument="-G" name="max_intron" type="integer" min="0" value="200000" label="Max intron size" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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76 <param argument="-n" name="min_syncmers" type="integer" min="1" value="5" label="Minimum number of syncmers in a chain" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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77 <param argument="-m" name="min_chain_score" type="integer" min="0" value="0" label="Minimum chaining score" />
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78 <param argument="-l" name="second_round_kmer_size" type="integer" min="1" value="5" label="K-mer size for second round of chaining" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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79 <param argument="-e" name="max_extension" type="integer" min="0" value="10000" label="Max extension for second round of chaining" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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80 <param argument="-p" name="score_ratio" type="float" min="0" max="1" value="0.5" label="Minimum secondary-to-primary score ratio" />
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81 <param argument="-N" name="max_secondary_alignments" type="integer" min="0" value="100" label="Max secondary alignments to consider" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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82 </section>
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83 <section name="alignment" title="Alignment">
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84 <param argument="-O" name="gap_open" type="integer" min="0" value="11" label="Gap open penalty" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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85 <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" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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86 <param argument="-J" name="intron_open" type="integer" min="0" value="31" label="Intron open penalty" />
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87 <param argument="-C" name="non_canonical_splice" type="integer" min="0" value="11" label="Penalty for non-canonical splicing" />
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88 <param argument="-F" name="frameshift" type="integer" min="0" value="15" label="Frameshift penalty" />
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89 <param argument="-B" name="end_bonus" type="integer" min="0" value="5" label="End bonus" />
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90 </section>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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91 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size" />
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92 </when>
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93 <when value="no">
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94 </when>
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95 </conditional>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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96 </inputs>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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97 <outputs>
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98 <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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99 <change_format>
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100 <when input="output_format" value="paf" format="paf" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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101 </change_format>
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102 </data>
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103 </outputs>
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104 <tests>
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105 <test expect_num_outputs="1">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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106 <conditional name="db">
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107 <param name="dbtype" value="fasta" />
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108 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
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109 </conditional>
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110 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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111 <output name="output_alignment" ftype="gff3">
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112 <assert_contents>
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113 <has_text text="ID=MP000001;Identity=1.0000;Positive=1.0000;Target=tr|O06302|O06302_MYCTU 1 126" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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114 <has_text text="Parent=MP000372;Target=tr|V5QPR5|V5QPR5_MYCTU 1 53" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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115 </assert_contents>
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116 </output>
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117 </test>
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118 <test expect_num_outputs="1">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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119 <conditional name="db">
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120 <param name="dbtype" value="fasta" />
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121 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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122 </conditional>
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123 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
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124 <param name="output_format" value="paf" />
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125 <output name="output_alignment" ftype="paf">
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126 <assert_contents>
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127 <has_text text="tr|O06302|O06302_MYCTU" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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128 <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" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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129 </assert_contents>
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130 </output>
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131 </test>
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132 <test expect_num_outputs="1">
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133 <conditional name="db">
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134 <param name="dbtype" value="fasta" />
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135 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" />
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136 </conditional>
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137 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" />
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138 <param name="output_format" value="gff" />
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139 <conditional name="adv">
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140 <param name="options" value="yes" />
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141 <param name="second_round_kmer_size" value="32" />
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142 </conditional>
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143 <output name="output_alignment" ftype="gff3">
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144 <assert_contents>
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145 <has_text text="##gff-version 3" />
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146 </assert_contents>
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147 </output>
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148 </test>
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149 </tests>
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150 <help><![CDATA[
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151 miniprot_ rapidly aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
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152 It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
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153
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154 **NOTE:** miniprot is in the early stages of development and should be considered experimental at this stage.
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155 .. _miniprot: https://github.com/lh3/miniprot
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156 ]]></help>
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157 </tool>