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comparison miniprot.xml @ 3:52bdc302299b draft

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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
comparison
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2:d518cf04b55c 3:52bdc302299b
28 -B $adv.alignment.end_bonus 28 -B $adv.alignment.end_bonus
29 -j $adv.alignment.splice_model 29 -j $adv.alignment.splice_model
30 #if str($adv.mapping.intron_size.mode) == 'manual' 30 #if str($adv.mapping.intron_size.mode) == 'manual'
31 -G $adv.mapping.intron_size.max_intron 31 -G $adv.mapping.intron_size.max_intron
32 #elif str($adv.mapping.intron_size.mode) == 'auto' 32 #elif str($adv.mapping.intron_size.mode) == 'auto'
33 -I 33 -I
34 #end if 34 #end if
35 35
36 #if str($adv.output.prefix) != 'MP' 36 #if str($adv.output.prefix) != 'MP'
37 -P '$adv.output.prefix' 37 -P '$adv.output.prefix'
38 #end if 38 #end if
39 $adv.output.print_unmapped_proteins 39 $adv.output.print_unmapped_proteins
40 --outn=$adv.output.outputs_per_query 40 --outn=$adv.output.outputs_per_query
41 --outc=$adv.output.output_fraction_query 41 --outc=$adv.output.output_fraction_query
42 --outs=$adv.output.output_score_least 42 --outs=$adv.output.output_score_least
43 $adv.output.output_translated_protein
44 $adv.output.output_no_cs
43 $adv.output.output_residue_alignment 45 $adv.output.output_residue_alignment
44 #end if 46 #end if
45 #if str($db.dbtype) == 'fasta' 47 #if str($db.dbtype) == 'fasta'
46 '$db.genomic_fasta' 48 '$db.genomic_fasta'
47 -k $db.kmer_size 49 -k $db.kmer_size
56 #else if str($output_format) == "gtf" 58 #else if str($output_format) == "gtf"
57 --gtf 59 --gtf
58 #end if 60 #end if
59 '$protein_fasta' > '$output_alignment' 61 '$protein_fasta' > '$output_alignment'
60 ]]></command> 62 ]]></command>
63
61 <inputs> 64 <inputs>
62 <conditional name="db"> 65 <conditional name="db">
63 <param name="dbtype" type="select" label="Database type" help="Build an index from FASTA or use a pre-indexed database"> 66 <param name="dbtype" type="select" label="Database type" help="Build an index from FASTA or use a pre-indexed database">
64 <option value="fasta" selected="true">FASTA</option> 67 <option value="fasta" selected="true">FASTA</option>
65 <option value="preindexed">Pre-indexed</option> 68 <option value="preindexed">Pre-indexed</option>
66 </param> 69 </param>
67 <when value="fasta"> 70 <when value="fasta">
68 <param name="genomic_fasta" type="data" format="fasta,fasta.gz" label="Genomic sequence (FASTA)" help="Genomic contigs / scaffolds to be aligned against in FASTA format" /> 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"/>
69 <param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing" /> 72 <param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing"/>
70 <param argument="-b" name="bits_per_block" type="integer" min="1" value="8" label="Number of bits per bin" help="Miniprot splits the genome into non-overlapping bins of 2^8 bp in size" /> 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"/>
71 <param argument="-M" name="modimisers" type="integer" value="1" label="Sample k-mers at a rate 1/2**INT" help="Increasing this option reduces peak memory but decreases sensitivity" /> 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"/>
72 <param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index" /> 75 <param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index"/>
73 </when> 76 </when>
74 <when value="preindexed"> 77 <when value="preindexed">
75 <!-- refine the datatype here once Miniprot index data type is in Galaxy --> 78 <!-- refine the datatype here once Miniprot index data type is in Galaxy -->
76 <param name="genomic_db" type="data" format="binary" label="Pre-indexed genomic database" help="A pre-indexed database built by miniprot" /> 79 <param name="genomic_db" type="data" format="binary" label="Pre-indexed genomic database" help="A pre-indexed database built by miniprot"/>
77 </when> 80 </when>
78 </conditional> 81 </conditional>
79 <param name="protein_fasta" type="data" format="fasta,fasta.gz" label="Protein sequence (FASTA)" help="Protein sequences to be aligned in FASTA format" /> 82 <param name="protein_fasta" type="data" format="fasta,fasta.gz" label="Protein sequence (FASTA)" help="Protein sequences to be aligned in FASTA format"/>
80 <param name="output_format" type="select" label="Output format" > 83 <param name="output_format" type="select" label="Output format">
81 <option value="gff" selected="true">GFF3</option> 84 <option value="gff" selected="true">GFF3</option>
82 <option value="paf">PAF</option> 85 <option value="paf">PAF</option>
83 <option value="gtf">GTF</option> 86 <option value="gtf">GTF</option>
84 </param> 87 </param>
85 <conditional name="adv"> 88 <conditional name="adv">
87 <option value="yes">Show</option> 90 <option value="yes">Show</option>
88 <option value="no" selected="true">Hide</option> 91 <option value="no" selected="true">Hide</option>
89 </param> 92 </param>
90 <when value="yes"> 93 <when value="yes">
91 <section name="mapping" title="Mapping"> 94 <section name="mapping" title="Mapping">
92 <param argument="-S" name="no_splicing" type="boolean" truevalue="-S" falsevalue="" checked="false" label="No splicing" help="No splicing (apply -G1000 -J1000 -e1000)" /> 95 <param argument="-S" name="no_splicing" type="boolean" truevalue="-S" falsevalue="" checked="false" label="No splicing" help="No splicing (apply -G1000 -J1000 -e1000)"/>
93 <param argument="-c" name="max_kmer" type="integer" min="1" value="20000" label="Max k-mer occurences" /> 96 <param argument="-c" name="max_kmer" type="integer" min="1" value="20000" label="Max k-mer occurences"/>
94 <param argument="-w" name="log_gap_penalty_weight" type="float" min="0" max="1" value="0.75" label="Log gap penalty weight" /> 97 <param argument="-w" name="log_gap_penalty_weight" type="float" min="0" max="1" value="0.75" label="Log gap penalty weight"/>
95 <param argument="-n" name="min_syncmers" type="integer" min="1" value="3" label="Minimum number of syncmers in a chain" /> 98 <param argument="-n" name="min_syncmers" type="integer" min="1" value="3" label="Minimum number of syncmers in a chain"/>
96 <param argument="-m" name="min_chain_score" type="integer" min="0" value="0" label="Minimum chaining score" /> 99 <param argument="-m" name="min_chain_score" type="integer" min="0" value="0" label="Minimum chaining score"/>
97 <param argument="-l" name="second_round_kmer_size" type="integer" min="1" value="5" label="K-mer size for second round of chaining" /> 100 <param argument="-l" name="second_round_kmer_size" type="integer" min="1" value="5" label="K-mer size for second round of chaining"/>
98 <param argument="-e" name="max_extension" type="integer" min="0" value="10000" label="Max extension for second round of chaining" /> 101 <param argument="-e" name="max_extension" type="integer" min="0" value="10000" label="Max extension for second round of chaining"/>
99 <param argument="-p" name="score_ratio" type="float" min="0" max="1" value="0.7" label="Minimum secondary-to-primary score ratio" /> 102 <param argument="-p" name="score_ratio" type="float" min="0" max="1" value="0.7" label="Minimum secondary-to-primary score ratio"/>
100 <param argument="-N" name="max_secondary_alignments" type="integer" min="0" value="30" label="Max secondary alignments to consider" /> 103 <param argument="-N" name="max_secondary_alignments" type="integer" min="0" value="30" label="Max secondary alignments to consider"/>
101 <conditional name="intron_size"> 104 <conditional name="intron_size">
102 <param name="mode" type="select" label="Maximum intron size"> 105 <param name="mode" type="select" label="Maximum intron size">
103 <option value="manual" selected="true">Manual</option> 106 <option value="manual" selected="true">Manual</option>
104 <option value="auto">Auto (3.6*sqrt)</option> 107 <option value="auto">Auto (3.6*sqrt)</option>
105 </param> 108 </param>
106 <when value="manual"> 109 <when value="manual">
107 <param argument="-G" name="max_intron" type="integer" min="0" value="200000" label="Maximum intron size" /> 110 <param argument="-G" name="max_intron" type="integer" min="0" value="200000" label="Maximum intron size"/>
108 </when> 111 </when>
109 <when value="auto" /> 112 <when value="auto"/>
110 </conditional> 113 </conditional>
111 </section> 114 </section>
112 <section name="alignment" title="Alignment"> 115 <section name="alignment" title="Alignment">
113 <param argument="-O" name="gap_open" type="integer" min="0" value="11" label="Gap open penalty" /> 116 <param argument="-O" name="gap_open" type="integer" min="0" value="11" label="Gap open penalty"/>
114 <param argument="-E" name="gap_extension" type="integer" min="0" value="1" label="Gap extension penalty" help="A k-long gap costs open_penalty+k*extension_penalty" /> 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"/>
115 <param argument="-J" name="intron_open" type="integer" min="0" value="29" label="Intron open penalty" /> 118 <param argument="-J" name="intron_open" type="integer" min="0" value="29" label="Intron open penalty"/>
116 <param argument="-C" name="non_canonical_splice" type="float" value="1" label="Weight of splice penalty; 0 to ignore splice signals" /> 119 <param argument="-C" name="non_canonical_splice" type="float" value="1" label="Weight of splice penalty; 0 to ignore splice signals"/>
117 <param argument="-F" name="frameshift" type="integer" min="0" value="23" label="Frameshift penalty" /> 120 <param argument="-F" name="frameshift" type="integer" min="0" value="23" label="Frameshift penalty"/>
118 <param argument="-B" name="end_bonus" type="integer" min="0" value="5" label="Bonus score for alignment reaching query ends" /> 121 <param argument="-B" name="end_bonus" type="integer" min="0" value="5" label="Bonus score for alignment reaching query ends"/>
119 <param argument="-j" name="splice_model" type="select" label="Splicing model for the target genome" help="2=mammal, 1=general, 0=none" > 122 <param argument="-j" name="splice_model" type="select" label="Splicing model for the target genome" help="2=mammal, 1=general, 0=none">
120 <option value="O" >None: No splicing model (0)</option> 123 <option value="O" >None: No splicing model (0)</option>
121 <option value="1" selected="true">General: Optimal splicing sequence: '|GTR...YAG|' (1)</option> 124 <option value="1" selected="true">General: Optimal splicing sequence: '|GTR...YAG|' (1)</option>
122 <option value="2">Mammal: Optimal splicing sequence: 'G|GTR...YYYNYAG|' (2)</option> 125 <option value="2">Mammal: Optimal splicing sequence: 'G|GTR...YYYNYAG|' (2)</option>
123 </param> 126 </param>
124 </section> 127 </section>
129 <add value="_" /> 132 <add value="_" />
130 <add value="-" /> 133 <add value="-" />
131 </valid> 134 </valid>
132 </sanitizer> 135 </sanitizer>
133 </param> 136 </param>
134 <param argument="-u" name="print_unmapped_proteins" type="boolean" truevalue="-u" falsevalue="" label="Print unmapped proteins" checked="false" /> 137 <param argument="-u" name="print_unmapped_proteins" type="boolean" truevalue="-u" falsevalue="" label="Print unmapped proteins" checked="false"/>
135 <param argument="--outn" name="outputs_per_query" type="integer" min="0" value="100" label="Outputs per query" help="The number of outputs will be the minimum of this and the max secondary alignments option" /> 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"/>
136 <param argument="--aln" name="output_residue_alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Output residue alignment" help="Only for GFF output" /> 139 <param argument="--aln" name="output_residue_alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Output residue alignment" help="Only for GFF output" />
137 <param argument="--outs" name="output_score_least" type="float" min="0" max="1" value="0.99" 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"/>
138 label="For each protein, only output alignments with a score higher than 'best_score' multiplied by this value"/> 141 <param argument="--outc" name="output_fraction_query" type="float" value="0.1" label="Output if at least this fraction of query is aligned"/>
139 <param argument="--outc" name="output_fraction_query" type="float" value="0.1" label="Output if at least this fraction of query is aligned" /> 142 <param argument="--trans" name="output_translated_protein" type="boolean" truevalue="--trans" falsevalue="" checked="false" label="Output translated protein sequences" help="Skipping frameshift"/>
140 </section> 143 <param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/>
141 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size" /> 144 </section>
145 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
142 </when> 146 </when>
143 <when value="no"> 147 <when value="no">
144 </when> 148 </when>
145 </conditional> 149 </conditional>
146 </inputs> 150 </inputs>
147 <outputs> 151 <outputs>
148 <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}"> 152 <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
149 <change_format> 153 <change_format>
150 <when input="output_format" value="paf" format="paf" /> 154 <when input="output_format" value="paf" format="paf"/>
151 <when input="output_format" value="gtf" format="gtf"/> 155 <when input="output_format" value="gtf" format="gtf"/>
152 </change_format> 156 </change_format>
153 </data> 157 </data>
154 </outputs> 158 </outputs>
155 <tests> 159 <tests>
156 <test expect_num_outputs="1"> 160 <test expect_num_outputs="1">
157 <conditional name="db"> 161 <conditional name="db">
158 <param name="dbtype" value="fasta" /> 162 <param name="dbtype" value="fasta" />
159 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" /> 163 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"/>
160 </conditional> 164 </conditional>
161 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" /> 165 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"/>
162 <output name="output_alignment" ftype="gff3"> 166 <output name="output_alignment" ftype="gff3">
163 <assert_contents> 167 <assert_contents>
164 <has_text text="ID=MP000001;Rank=1;Identity=0.3420;Positive=0.5104;Target=tr|I6YGH7|I6YGH7_MYCTU 1 375" /> 168 <has_text text="ID=MP000001;Rank=1;Identity=0.3420;Positive=0.5104;Target=tr|I6YGH7|I6YGH7_MYCTU 1 375"/>
165 <has_text text="ID=MP000066;Rank=1;Identity=0.3613;Positive=0.5178;Target=sp|P9WQE5|PPSB_MYCTU 1 1214" /> 169 <has_text text="ID=MP000066;Rank=1;Identity=0.3613;Positive=0.5178;Target=sp|P9WQE5|PPSB_MYCTU 1 1214"/>
166 </assert_contents> 170 </assert_contents>
167 </output> 171 </output>
168 </test> 172 </test>
173 <test expect_num_outputs="1">
174 <conditional name="db">
175 <param name="dbtype" value="fasta"/>
176 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"/>
177 </conditional>
178 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"/>
179 <param name="output_format" value="paf"/>
180 <output name="output_alignment" ftype="paf">
181 <assert_contents>
182 <has_text text="tr|O06302|O06302_MYCTU" />
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"/>
184 </assert_contents>
185 </output>
186 </test>
169 <test expect_num_outputs="1"> 187 <test expect_num_outputs="1">
170 <conditional name="db"> 188 <conditional name="db">
171 <param name="dbtype" value="fasta" /> 189 <param name="dbtype" value="fasta" />
172 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" /> 190 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"/>
173 </conditional> 191 </conditional>
174 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" /> 192 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"/>
175 <param name="output_format" value="paf" /> 193 <param name="output_format" value="gff" />
194 <conditional name="adv">
195 <param name="options" value="yes" />
196 <param name="second_round_kmer_size" value="32"/>
197 </conditional>
198 <output name="output_alignment" ftype="gff3">
199 <assert_contents>
200 <has_text text="##gff-version 3" />
201 </assert_contents>
202 </output>
203 </test>
204 <test expect_num_outputs="1">
205 <conditional name="db">
206 <param name="dbtype" value="fasta"></param>
207 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
208 </conditional>
209 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
210 <param name="output_format" value="gtf"></param>
211 <conditional name="adv">
212 <param name="options" value="yes"></param>
213 <param name="second_round_kmer_size" value="32"></param>
214 </conditional>
215 <output name="output_alignment" ftype="gtf">
216 <assert_contents>
217 <has_text text="NC_000962.3" />
218 <has_text text='transcript_id "MPT000004"; gene_id "MPG000004"'/>
219 </assert_contents>
220 </output>
221 </test>
222 <test expect_num_outputs="1">
223 <conditional name="db">
224 <param name="dbtype" value="fasta"></param>
225 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
226 </conditional>
227 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
228 <param name="output_format" value="gff"></param>
229 <conditional name="adv">
230 <param name="options" value="yes"/>
231 <section name="output">
232 <param name="output_translated_protein" value="true"/>
233 </section>
234 </conditional>
235 <output name="output_alignment" ftype="gff3">
236 <assert_contents>
237 <has_text text="tr|I6YGH7|I6YGH7_MYCTU" />
238 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
239 <has_n_lines n="1633"/>
240 </assert_contents>
241 </output>
242 </test>
243 <test expect_num_outputs="1">
244 <conditional name="db">
245 <param name="dbtype" value="fasta"></param>
246 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
247 </conditional>
248 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
249 <param name="output_format" value="gtf"></param>
250 <conditional name="adv">
251 <param name="options" value="yes"></param>
252 <section name="output">
253 <param name="output_translated_protein" value="true"/>
254 </section>
255 </conditional>
256 <output name="output_alignment" ftype="gtf">
257 <assert_contents>
258 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
259 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
260 <has_text text="NC_000962.3"/>
261 <has_n_lines n="2172"/>
262 </assert_contents>
263 </output>
264 </test>
265 <test expect_num_outputs="1">
266 <conditional name="db">
267 <param name="dbtype" value="fasta"></param>
268 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
269 </conditional>
270 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
271 <param name="output_format" value="paf"></param>
272 <conditional name="adv">
273 <param name="options" value="yes"></param>
274 <section name="output">
275 <param name="output_translated_protein" value="true"/>
276 </section>
277 </conditional>
176 <output name="output_alignment" ftype="paf"> 278 <output name="output_alignment" ftype="paf">
177 <assert_contents> 279 <assert_contents>
178 <has_text text="tr|O06302|O06302_MYCTU" /> 280 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
179 <has_text text="cs:Z::29*agcG:3*gtgA:5*ccgA:9*accS:1*gccV:4*cagL:1*gtcS:3*gtcA*gtcI*accA*gccG:8*gccS:2*ggtA:5*gccI*agcG:1*ctgA:4*gccV:5*gggL:1*gtgS:2" /> 281 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
180 </assert_contents> 282 <has_text text="sp|O05779|FTSE_MYCTU"/>
181 </output> 283 <has_n_lines n="650"/>
182 </test> 284 </assert_contents>
183 <test expect_num_outputs="1"> 285 </output>
184 <conditional name="db"> 286 </test>
185 <param name="dbtype" value="fasta" /> 287 <test expect_num_outputs="1">
186 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta" /> 288 <conditional name="db">
187 </conditional> 289 <param name="dbtype" value="fasta"></param>
188 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta" /> 290 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
189 <param name="output_format" value="gff" /> 291 </conditional>
190 <conditional name="adv"> 292 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
191 <param name="options" value="yes" /> 293 <param name="output_format" value="paf"></param>
192 <param name="second_round_kmer_size" value="32" /> 294 <conditional name="adv">
295 <param name="options" value="yes"></param>
296 <section name="output">
297 <param name="output_no_cs" value="true"/>
298 </section>
299 </conditional>
300 <output name="output_alignment" ftype="paf">
301 <assert_contents>
302 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
303 <has_text text="cg:Z:17M1D20M14I2M1I24M1I195M4D61M6D40M"/>
304 <has_text text="cg:Z:188M3I4M5I11M6I3M1I31M2D1M282U7M1D6M3D28M3I20M1D52M3D4M1D24M2I8M5I5M2I32M1D21M"/>
305 </assert_contents>
306 </output>
307 </test>
308 <test expect_num_outputs="1">
309 <conditional name="db">
310 <param name="dbtype" value="fasta"></param>
311 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
312 </conditional>
313 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
314 <param name="output_format" value="gff"></param>
315 <conditional name="adv">
316 <param name="options" value="yes"></param>
317 <section name="output">
318 <param name="output_no_cs" value="true"/>
319 </section>
193 </conditional> 320 </conditional>
194 <output name="output_alignment" ftype="gff3"> 321 <output name="output_alignment" ftype="gff3">
195 <assert_contents> 322 <assert_contents>
196 <has_text text="##gff-version 3" /> 323 <has_text text="##gff-version 3"/>
197 </assert_contents> 324 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
198 </output> 325 <has_text text="cg:Z:17M1D20M14I2M1I24M1I195M4D61M6D40M"/>
199 </test> 326 </assert_contents>
200 327 </output>
328 </test>
201 <test expect_num_outputs="1"> 329 <test expect_num_outputs="1">
202 <conditional name="db"> 330 <conditional name="db">
203 <param name="dbtype" value="fasta"></param> 331 <param name="dbtype" value="fasta"></param>
204 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param> 332 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
205 </conditional> 333 </conditional>
206 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param> 334 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
207 <param name="output_format" value="gtf"></param> 335 <param name="output_format" value="gtf"></param>
208 <conditional name="adv"> 336 <conditional name="adv">
209 <param name="options" value="yes"></param> 337 <param name="options" value="yes"></param>
210 <param name="second_round_kmer_size" value="32"></param> 338 <section name="output">
339 <param name="output_no_cs" value="true"/>
340 </section>
211 </conditional> 341 </conditional>
212 <output name="output_alignment" ftype="gtf"> 342 <output name="output_alignment" ftype="gtf">
213 <assert_contents> 343 <assert_contents>
214 <has_text text="NC_000962.3" /> 344 <has_text text="NC_000962.3"/>
215 <has_text text='transcript_id "MPT000004"; gene_id "MPG000004"' /> 345 <has_text text='gene_id "MPG000001"'/>
216 </assert_contents> 346 </assert_contents>
217 </output> 347 </output>
218 </test> 348 </test>
219
220
221 </tests> 349 </tests>
350
222 <help><![CDATA[ 351 <help><![CDATA[
223 miniprot_ rapidly aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. 352 miniprot_ rapidly aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
224 It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. 353 It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
225 354
226 While an index of the genome to be mapped to can be built "on the fly", the Miniprot index tool can pre-index a genome 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