annotate miniprot.xml @ 3:52bdc302299b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
author iuc
date Thu, 13 Jul 2023 09:37:56 +0000
parents d518cf04b55c
children 00b22efdd100
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ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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1 <?xml version="1.0"?>
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2 <tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy0" profile="21.05">
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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>
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6 </macros>
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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>
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10 <command detect_errors="exit_code"><![CDATA[
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11 miniprot
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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"
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14 $adv.mapping.no_splicing
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15 -c $adv.mapping.max_kmer
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16 -n $adv.mapping.min_syncmers
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17 -m $adv.mapping.min_chain_score
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18 -l $adv.mapping.second_round_kmer_size
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19 -e $adv.mapping.max_extension
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20 -p $adv.mapping.score_ratio
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21 -N $adv.mapping.max_secondary_alignments
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22 -w $adv.mapping.log_gap_penalty_weight
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23 -O $adv.alignment.gap_open
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24 -E $adv.alignment.gap_extension
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25 -J $adv.alignment.intron_open
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26 -C $adv.alignment.non_canonical_splice
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27 -F $adv.alignment.frameshift
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28 -B $adv.alignment.end_bonus
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29 -j $adv.alignment.splice_model
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30 #if str($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'
3
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33 -I
2
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34 #end if
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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($adv.output.prefix) != 'MP'
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37 -P '$adv.output.prefix'
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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 $adv.output.print_unmapped_proteins
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40 --outn=$adv.output.outputs_per_query
2
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41 --outc=$adv.output.output_fraction_query
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42 --outs=$adv.output.output_score_least
3
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43 $adv.output.output_translated_protein
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44 $adv.output.output_no_cs
2
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45 $adv.output.output_residue_alignment
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46 #end if
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47 #if str($db.dbtype) == 'fasta'
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48 '$db.genomic_fasta'
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49 -k $db.kmer_size
2
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50 -b $db.bits_per_block
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51 -M $db.modimisers
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52 -L $db.min_ORF
0
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53 #else
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54 '$db.genomic_db'
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55 #end if
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56 #if str($output_format) == "gff"
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57 --gff
2
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58 #else if str($output_format) == "gtf"
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59 --gtf
0
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60 #end if
2
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61 '$protein_fasta' > '$output_alignment'
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62 ]]></command>
3
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63
0
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64 <inputs>
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65 <conditional name="db">
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66 <param name="dbtype" type="select" label="Database type" help="Build an index from FASTA or use a pre-indexed database">
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67 <option value="fasta" selected="true">FASTA</option>
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68 <option value="preindexed">Pre-indexed</option>
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69 </param>
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70 <when value="fasta">
3
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71 <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"/>
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72 <param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing"/>
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73 <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"/>
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74 <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"/>
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75 <param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index"/>
0
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76 </when>
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77 <when value="preindexed">
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78 <!-- refine the datatype here once Miniprot index data type is in Galaxy -->
3
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79 <param name="genomic_db" type="data" format="binary" label="Pre-indexed genomic database" help="A pre-indexed database built by miniprot"/>
0
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80 </when>
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81 </conditional>
3
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82 <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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83 <param name="output_format" type="select" label="Output format">
0
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84 <option value="gff" selected="true">GFF3</option>
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85 <option value="paf">PAF</option>
2
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86 <option value="gtf">GTF</option>
0
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87 </param>
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88 <conditional name="adv">
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89 <param name="options" type="select" label="Advanced options">
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90 <option value="yes">Show</option>
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91 <option value="no" selected="true">Hide</option>
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92 </param>
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93 <when value="yes">
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94 <section name="mapping" title="Mapping">
3
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95 <param argument="-S" name="no_splicing" type="boolean" truevalue="-S" falsevalue="" checked="false" label="No splicing" help="No splicing (apply -G1000 -J1000 -e1000)"/>
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96 <param argument="-c" name="max_kmer" type="integer" min="1" value="20000" label="Max k-mer occurences"/>
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97 <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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98 <param argument="-n" name="min_syncmers" type="integer" min="1" value="3" label="Minimum number of syncmers in a chain"/>
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99 <param argument="-m" name="min_chain_score" type="integer" min="0" value="0" label="Minimum chaining score"/>
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100 <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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101 <param argument="-e" name="max_extension" type="integer" min="0" value="10000" label="Max extension for second round of chaining"/>
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102 <param argument="-p" name="score_ratio" type="float" min="0" max="1" value="0.7" label="Minimum secondary-to-primary score ratio"/>
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103 <param argument="-N" name="max_secondary_alignments" type="integer" min="0" value="30" label="Max secondary alignments to consider"/>
2
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104 <conditional name="intron_size">
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105 <param name="mode" type="select" label="Maximum intron size">
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106 <option value="manual" selected="true">Manual</option>
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107 <option value="auto">Auto (3.6*sqrt)</option>
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108 </param>
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109 <when value="manual">
3
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110 <param argument="-G" name="max_intron" type="integer" min="0" value="200000" label="Maximum intron size"/>
2
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111 </when>
3
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112 <when value="auto"/>
2
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113 </conditional>
0
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114 </section>
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115 <section name="alignment" title="Alignment">
3
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116 <param argument="-O" name="gap_open" type="integer" min="0" value="11" label="Gap open penalty"/>
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117 <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"/>
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118 <param argument="-J" name="intron_open" type="integer" min="0" value="29" label="Intron open penalty"/>
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119 <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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120 <param argument="-F" name="frameshift" type="integer" min="0" value="23" label="Frameshift penalty"/>
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121 <param argument="-B" name="end_bonus" type="integer" min="0" value="5" label="Bonus score for alignment reaching query ends"/>
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122 <param argument="-j" name="splice_model" type="select" label="Splicing model for the target genome" help="2=mammal, 1=general, 0=none">
2
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123 <option value="O" >None: No splicing model (0)</option>
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124 <option value="1" selected="true">General: Optimal splicing sequence: '|GTR...YAG|' (1)</option>
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125 <option value="2">Mammal: Optimal splicing sequence: 'G|GTR...YYYNYAG|' (2)</option>
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126 </param>
0
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127 </section>
1
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128 <section name="output" title="Output">
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129 <param argument="-P" name="prefix" type="text" label="Prefix for IDs in GFF3 output" value="MP">
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130 <sanitizer invalid_char="">
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131 <valid initial="string.ascii_letters,string.digits">
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132 <add value="_" />
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133 <add value="-" />
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134 </valid>
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135 </sanitizer>
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136 </param>
3
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137 <param argument="-u" name="print_unmapped_proteins" type="boolean" truevalue="-u" falsevalue="" label="Print unmapped proteins" checked="false"/>
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138 <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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139 <param argument="--aln" name="output_residue_alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Output residue alignment" help="Only for GFF output" />
3
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140 <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"/>
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141 <param argument="--outc" name="output_fraction_query" type="float" value="0.1" label="Output if at least this fraction of query is aligned"/>
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142 <param argument="--trans" name="output_translated_protein" type="boolean" truevalue="--trans" falsevalue="" checked="false" label="Output translated protein sequences" help="Skipping frameshift"/>
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143 <param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/>
1
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144 </section>
3
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145 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
0
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146 </when>
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147 <when value="no">
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148 </when>
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149 </conditional>
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150 </inputs>
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151 <outputs>
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152 <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
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153 <change_format>
3
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154 <when input="output_format" value="paf" format="paf"/>
2
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155 <when input="output_format" value="gtf" format="gtf"/>
0
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156 </change_format>
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157 </data>
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158 </outputs>
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159 <tests>
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160 <test expect_num_outputs="1">
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161 <conditional name="db">
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162 <param name="dbtype" value="fasta" />
3
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163 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"/>
0
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164 </conditional>
3
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165 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"/>
0
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166 <output name="output_alignment" ftype="gff3">
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167 <assert_contents>
3
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168 <has_text text="ID=MP000001;Rank=1;Identity=0.3420;Positive=0.5104;Target=tr|I6YGH7|I6YGH7_MYCTU 1 375"/>
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169 <has_text text="ID=MP000066;Rank=1;Identity=0.3613;Positive=0.5178;Target=sp|P9WQE5|PPSB_MYCTU 1 1214"/>
0
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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170 </assert_contents>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
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171 </output>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
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172 </test>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
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diff changeset
173 <test expect_num_outputs="1">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
174 <conditional name="db">
3
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
175 <param name="dbtype" value="fasta"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
176 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"/>
0
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
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diff changeset
177 </conditional>
3
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
178 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
179 <param name="output_format" value="paf"/>
0
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
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180 <output name="output_alignment" ftype="paf">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
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181 <assert_contents>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
182 <has_text text="tr|O06302|O06302_MYCTU" />
3
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
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183 <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"/>
0
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
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184 </assert_contents>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
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185 </output>
2
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
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186 </test>
0
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
187 <test expect_num_outputs="1">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
188 <conditional name="db">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
189 <param name="dbtype" value="fasta" />
3
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
190 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"/>
0
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
191 </conditional>
3
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
192 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"/>
0
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
193 <param name="output_format" value="gff" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
194 <conditional name="adv">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
195 <param name="options" value="yes" />
3
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
196 <param name="second_round_kmer_size" value="32"/>
0
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
197 </conditional>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
198 <output name="output_alignment" ftype="gff3">
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
199 <assert_contents>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
200 <has_text text="##gff-version 3" />
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
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201 </assert_contents>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
202 </output>
ef712a5e9834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
iuc
parents:
diff changeset
203 </test>
2
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
204 <test expect_num_outputs="1">
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
205 <conditional name="db">
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
206 <param name="dbtype" value="fasta"></param>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
207 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
208 </conditional>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
209 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
210 <param name="output_format" value="gtf"></param>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
211 <conditional name="adv">
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
212 <param name="options" value="yes"></param>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
213 <param name="second_round_kmer_size" value="32"></param>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
214 </conditional>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
215 <output name="output_alignment" ftype="gtf">
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
216 <assert_contents>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
217 <has_text text="NC_000962.3" />
3
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
218 <has_text text='transcript_id "MPT000004"; gene_id "MPG000004"'/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
219 </assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
220 </output>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
221 </test>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
222 <test expect_num_outputs="1">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
223 <conditional name="db">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
224 <param name="dbtype" value="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
225 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
226 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
227 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
228 <param name="output_format" value="gff"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
229 <conditional name="adv">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
230 <param name="options" value="yes"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
231 <section name="output">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
232 <param name="output_translated_protein" value="true"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
233 </section>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
234 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
235 <output name="output_alignment" ftype="gff3">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
236 <assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
237 <has_text text="tr|I6YGH7|I6YGH7_MYCTU" />
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
238 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
239 <has_n_lines n="1633"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
240 </assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
241 </output>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
242 </test>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
243 <test expect_num_outputs="1">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
244 <conditional name="db">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
245 <param name="dbtype" value="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
246 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
247 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
248 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
249 <param name="output_format" value="gtf"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
250 <conditional name="adv">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
251 <param name="options" value="yes"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
252 <section name="output">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
253 <param name="output_translated_protein" value="true"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
254 </section>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
255 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
256 <output name="output_alignment" ftype="gtf">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
257 <assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
258 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
259 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
260 <has_text text="NC_000962.3"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
261 <has_n_lines n="2172"/>
2
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
262 </assert_contents>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
263 </output>
d518cf04b55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit bda011acaca773960c85bfa1288fa8b74cfabb15
iuc
parents: 1
diff changeset
264 </test>
3
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
265 <test expect_num_outputs="1">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
266 <conditional name="db">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
267 <param name="dbtype" value="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
268 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
269 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
270 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
271 <param name="output_format" value="paf"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
272 <conditional name="adv">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
273 <param name="options" value="yes"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
274 <section name="output">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
275 <param name="output_translated_protein" value="true"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
276 </section>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
277 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
278 <output name="output_alignment" ftype="paf">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
279 <assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
280 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
281 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
282 <has_text text="sp|O05779|FTSE_MYCTU"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
283 <has_n_lines n="650"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
284 </assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
285 </output>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
286 </test>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
287 <test expect_num_outputs="1">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
288 <conditional name="db">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
289 <param name="dbtype" value="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
290 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
291 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
292 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
293 <param name="output_format" value="paf"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
294 <conditional name="adv">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
295 <param name="options" value="yes"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
296 <section name="output">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
297 <param name="output_no_cs" value="true"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
298 </section>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
299 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
300 <output name="output_alignment" ftype="paf">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
301 <assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
302 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
303 <has_text text="cg:Z:17M1D20M14I2M1I24M1I195M4D61M6D40M"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
304 <has_text text="cg:Z:188M3I4M5I11M6I3M1I31M2D1M282U7M1D6M3D28M3I20M1D52M3D4M1D24M2I8M5I5M2I32M1D21M"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
305 </assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
306 </output>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
307 </test>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
308 <test expect_num_outputs="1">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
309 <conditional name="db">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
310 <param name="dbtype" value="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
311 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
312 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
313 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
314 <param name="output_format" value="gff"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
315 <conditional name="adv">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
316 <param name="options" value="yes"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
317 <section name="output">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
318 <param name="output_no_cs" value="true"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
319 </section>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
320 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
321 <output name="output_alignment" ftype="gff3">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
322 <assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
323 <has_text text="##gff-version 3"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
324 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
325 <has_text text="cg:Z:17M1D20M14I2M1I24M1I195M4D61M6D40M"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
326 </assert_contents>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
327 </output>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
328 </test>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
329 <test expect_num_outputs="1">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
330 <conditional name="db">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
331 <param name="dbtype" value="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
332 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
333 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
334 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
335 <param name="output_format" value="gtf"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
336 <conditional name="adv">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
337 <param name="options" value="yes"></param>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
338 <section name="output">
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
339 <param name="output_no_cs" value="true"/>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
340 </section>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
parents: 2
diff changeset
341 </conditional>
52bdc302299b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 7686c033edb974379f855d2563149d56920f063e
iuc
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342 <output name="output_alignment" ftype="gtf">
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343 <assert_contents>
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344 <has_text text="NC_000962.3"/>
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345 <has_text text='gene_id "MPG000001"'/>
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346 </assert_contents>
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347 </output>
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348 </test>
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349 </tests>
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350
0
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351 <help><![CDATA[
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352 miniprot_ rapidly aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
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353 It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
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354
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355 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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356 and will result in faster performance if the genome index is reused multiple times.
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357
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358 For details of the algorithm and some insight into how parameters can be tuned see this overview_.
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359
0
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360 .. _miniprot: https://github.com/lh3/miniprot
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361 .. _overview: https://github.com/lh3/miniprot#algorithm-overview
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362 ]]></help>
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363 <expand macro="citation"></expand>
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364 </tool>