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comparison miniprot.xml @ 4:7af86e8e3d3b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit c5721c97d7ec8c3a53725dbb685bbcdc677a75a9
author iuc
date Fri, 25 Apr 2025 13:04:42 +0000
parents 7a5f7c743b92
children
comparison
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3:7a5f7c743b92 4:7af86e8e3d3b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy0" profile="21.05"> 2 <tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
3 <description>align a protein sequence against a genome with affine gap penalty, splicing and frameshift</description> 3 <description>align a protein sequence against a genome with affine gap penalty, splicing and frameshift</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <requirements> 7 <expand macro="xrefs"/>
8 <requirement type="package" version="@TOOL_VERSION@">miniprot</requirement> 8 <expand macro="requirements"/>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 miniprot 10 miniprot
12 -t \${GALAXY_SLOTS:-1} 11 -t \${GALAXY_SLOTS:-1}
13 #if str($adv.options) == "yes" 12 #if str($adv.options) == "yes"
14 $adv.mapping.no_splicing 13 $adv.mapping.no_splicing
24 -E $adv.alignment.gap_extension 23 -E $adv.alignment.gap_extension
25 -J $adv.alignment.intron_open 24 -J $adv.alignment.intron_open
26 -C $adv.alignment.non_canonical_splice 25 -C $adv.alignment.non_canonical_splice
27 -F $adv.alignment.frameshift 26 -F $adv.alignment.frameshift
28 -B $adv.alignment.end_bonus 27 -B $adv.alignment.end_bonus
29 -j $adv.alignment.splice_model 28 -j $adv.alignment.splice_model
29 #if str($adv.ncbi_table) !=""
30 -T '$adv.ncbi_table'
31 #end if
30 #if str($adv.mapping.intron_size.mode) == 'manual' 32 #if str($adv.mapping.intron_size.mode) == 'manual'
31 -G $adv.mapping.intron_size.max_intron 33 -G $adv.mapping.intron_size.max_intron
32 #elif str($adv.mapping.intron_size.mode) == 'auto' 34 #elif str($adv.mapping.intron_size.mode) == 'auto'
33 -I 35 -I
34 #end if 36 #end if
70 <when value="fasta"> 72 <when value="fasta">
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"/> 73 <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"/>
72 <param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing"/> 74 <param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing"/>
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"/> 75 <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"/>
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"/> 76 <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"/>
75 <param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index"/> 77 <param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index"/>
76 </when> 78 </when>
77 <when value="preindexed"> 79 <when value="preindexed">
78 <!-- refine the datatype here once Miniprot index data type is in Galaxy --> 80 <!-- refine the datatype here once Miniprot index data type is in Galaxy -->
79 <param name="genomic_db" type="data" format="binary" label="Pre-indexed genomic database" help="A pre-indexed database built by miniprot"/> 81 <param name="genomic_db" type="data" format="binary" label="Pre-indexed genomic database" help="A pre-indexed database built by miniprot"/>
80 </when> 82 </when>
141 <param argument="--outc" name="output_fraction_query" type="float" value="0.1" label="Output if at least this fraction of query is aligned"/> 143 <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"/> 144 <param argument="--trans" name="output_translated_protein" type="boolean" truevalue="--trans" falsevalue="" checked="false" label="Output translated protein sequences" help="Skipping frameshift"/>
143 <param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/> 145 <param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/>
144 </section> 146 </section>
145 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/> 147 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
148 <param argument="-T" name="ncbi_table" type="select" optional="true" label="Enter NCBI translation table">
149 <option value="1">1 Standard code</option>
150 <option value="2">2 Vertebrate mitochondrial</option>
151 <option value="3">3 Yeast mitochondrial</option>
152 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option>
153 <option value="5">5 Invertebrate mitochondrial</option>
154 <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option>
155 <option value="9">9 Echinoderm and flatworm mitochondrial</option>
156 <option value="10">10 Euplotid nuclear</option>
157 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option>
158 <option value="12">12 Alternative yeast nuclear</option>
159 <option value="13">13 Ascidian mitochondrial</option>
160 <option value="14">14 Alternative flatworm mitochondrial</option>
161 <option value="16">16 Chlorophycean mitochondrial</option>
162 <option value="21">21 Trematode Mitochondrial</option>
163 <option value="22">22 Scenedesmus obliquus Mitochondrial</option>
164 <option value="23">23 Thraustochytrium Mitochondrial</option>
165 <option value="24">24 Rhabdopleuridae Mitochondrial</option>
166 <option value="25">25 Candidate Division SR1 and Gracilibacteria</option>
167 <option value="26">26 Pachysolen tannophilus Nuclear</option>
168 <option value="27">27 Karyorelict Nuclear</option>
169 <option value="28">28 Condylostoma Nuclear</option>
170 <option value="29">29 Mesodinium nuclear</option>
171 <option value="30">30 Peritrich nuclear</option>
172 <option value="31">31 Blastocrithidia nuclear</option>
173 <option value="33">33 Cephalodiscidae mitochondrial</option>
174 </param>
146 </when> 175 </when>
147 <when value="no"> 176 <when value="no">
148 </when> 177 </when>
149 </conditional> 178 </conditional>
179
150 </inputs> 180 </inputs>
151 <outputs> 181 <outputs>
152 <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}"> 182 <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
153 <change_format> 183 <change_format>
154 <when input="output_format" value="paf" format="paf"/> 184 <when input="output_format" value="paf" format="paf"/>
234 </conditional> 264 </conditional>
235 <output name="output_alignment" ftype="gff3"> 265 <output name="output_alignment" ftype="gff3">
236 <assert_contents> 266 <assert_contents>
237 <has_text text="tr|I6YGH7|I6YGH7_MYCTU" /> 267 <has_text text="tr|I6YGH7|I6YGH7_MYCTU" />
238 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/> 268 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
239 <has_n_lines n="1633"/> 269 <has_n_lines n="1647"/>
240 </assert_contents> 270 </assert_contents>
241 </output> 271 </output>
242 </test> 272 </test>
243 <test expect_num_outputs="1"> 273 <test expect_num_outputs="1">
244 <conditional name="db"> 274 <conditional name="db">
256 <output name="output_alignment" ftype="gtf"> 286 <output name="output_alignment" ftype="gtf">
257 <assert_contents> 287 <assert_contents>
258 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/> 288 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
259 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/> 289 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
260 <has_text text="NC_000962.3"/> 290 <has_text text="NC_000962.3"/>
261 <has_n_lines n="2172"/> 291 <has_n_lines n="2196"/>
262 </assert_contents> 292 </assert_contents>
263 </output> 293 </output>
264 </test> 294 </test>
265 <test expect_num_outputs="1"> 295 <test expect_num_outputs="1">
266 <conditional name="db"> 296 <conditional name="db">
278 <output name="output_alignment" ftype="paf"> 308 <output name="output_alignment" ftype="paf">
279 <assert_contents> 309 <assert_contents>
280 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/> 310 <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
281 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/> 311 <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
282 <has_text text="sp|O05779|FTSE_MYCTU"/> 312 <has_text text="sp|O05779|FTSE_MYCTU"/>
283 <has_n_lines n="650"/> 313 <has_n_lines n="654"/>
284 </assert_contents> 314 </assert_contents>
285 </output> 315 </output>
286 </test> 316 </test>
287 <test expect_num_outputs="1"> 317 <test expect_num_outputs="1">
288 <conditional name="db"> 318 <conditional name="db">
331 <param name="dbtype" value="fasta"></param> 361 <param name="dbtype" value="fasta"></param>
332 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param> 362 <param name="genomic_fasta" value="input_genome.fasta.gz" ftype="fasta"></param>
333 </conditional> 363 </conditional>
334 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param> 364 <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
335 <param name="output_format" value="gtf"></param> 365 <param name="output_format" value="gtf"></param>
366 <param name="ncbi_table" value="1"></param>
336 <conditional name="adv"> 367 <conditional name="adv">
337 <param name="options" value="yes"></param> 368 <param name="options" value="yes"></param>
338 <section name="output"> 369 <section name="output">
339 <param name="output_no_cs" value="true"/> 370 <param name="output_no_cs" value="true"/>
340 </section> 371 </section>