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comparison minimap2.xml @ 14:4f88b74199bf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
author iuc
date Fri, 11 Oct 2019 13:26:54 -0400
parents ba69511b9e66
children 6d5a7cc63314
comparison
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13:ba69511b9e66 14:4f88b74199bf
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@" profile="17.01"> 2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy0" profile="17.01">
3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> 3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
4 <macros> 4 <macros>
5 <token name="@TOOL_VERSION@">2.17</token> 5 <token name="@TOOL_VERSION@">2.17</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
15 ln -f -s '$reference_source.ref_file' reference.fa && 15 ln -f -s '$reference_source.ref_file' reference.fa &&
16 #else: 16 #else:
17 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && 17 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
18 #end if 18 #end if
19 minimap2 19 minimap2
20 -x $analysis_type_selector 20 #if str($analysis_type_selector) == 'self-homology':
21 -DP -k19 -w19 -m200
22 #else
23 -x $analysis_type_selector
24 #end if
21 ## indexing options 25 ## indexing options
22 $indexing_options.H 26 $indexing_options.H
23 #if $indexing_options.k: 27 #if $indexing_options.k:
24 -k $indexing_options.k 28 -k $indexing_options.k
25 #end if 29 #end if
111 #end if 115 #end if
112 #if $io_options.output_format == 'BAM': 116 #if $io_options.output_format == 'BAM':
113 -a 117 -a
114 | samtools sort 118 | samtools sort
115 -@\${GALAXY_SLOTS:-2} 119 -@\${GALAXY_SLOTS:-2}
120 -T "\${TMPDIR:-.}"
116 -O $io_options.output_format 121 -O $io_options.output_format
117 -o '$alignment_output' 122 -o '$alignment_output'
118 #else if $io_options.output_format == 'CRAM': 123 #else if $io_options.output_format == 'CRAM':
119 -a 124 -a
120 | samtools sort 125 | samtools sort
126 -T "\${TMPDIR:-.}"
121 -@\${GALAXY_SLOTS:-2} 127 -@\${GALAXY_SLOTS:-2}
122 -O $io_options.output_format 128 -O $io_options.output_format
123 $io_options.eqx 129 $io_options.eqx
124 --reference reference.fa 130 --reference reference.fa
125 --output-fmt-option no_ref 131 --output-fmt-option no_ref
184 <option value="asm5">Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%.</option> 190 <option value="asm5">Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%.</option>
185 <option value="asm10">Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence.</option> 191 <option value="asm10">Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence.</option>
186 <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence.</option> 192 <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence.</option>
187 <option value="splice">Long-read spliced alignment (-k15 -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as the `N' CIGAR operator 2) long insertions are disabled 3) deletion and insertion gap costs are different during chaining 4) the computation of the `ms' tag ignores introns to demote hits to pseudogenes.</option> 193 <option value="splice">Long-read spliced alignment (-k15 -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as the `N' CIGAR operator 2) long insertions are disabled 3) deletion and insertion gap costs are different during chaining 4) the computation of the `ms' tag ignores introns to demote hits to pseudogenes.</option>
188 <option value="sr">Short single-end reads without splicing (-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no)</option> 194 <option value="sr">Short single-end reads without splicing (-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no)</option>
195 <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200)</option>
189 </param> 196 </param>
190 <section name="mapping_options" title="Set advanced mapping options" help="Sets -f, -g, -G, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False"> 197 <section name="mapping_options" title="Set advanced mapping options" help="Sets -f, -g, -G, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False">
191 <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/> 198 <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
192 <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" /> 199 <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />
193 <param argument="-g" type="integer" value="" optional="true" label="stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/> 200 <param argument="-g" type="integer" value="" optional="true" label="stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/>
329 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" /> 336 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" />
330 <param name="analysis_type_selector" value="ava-ont"/> 337 <param name="analysis_type_selector" value="ava-ont"/>
331 <param name="output_format" value="paf"/> 338 <param name="output_format" value="paf"/>
332 <output name="alignment_output" ftype="tabular" file="mini_reads.paf" /> 339 <output name="alignment_output" ftype="tabular" file="mini_reads.paf" />
333 </test> 340 </test>
341 <test>
342 <!-- test self-homology mode -->
343 <param name="reference_source_selector" value="history" />
344 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
345 <param name="fastq_input_selector" value="single" />
346 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
347 <param name="analysis_type_selector" value="self-homology" />
348 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" />
349 </test>
334 </tests> 350 </tests>
335 <help> 351 <help>
336 352
337 Users’ Guide 353 Users’ Guide
338 ------------ 354 ------------
445 Full genome/assembly alignment 461 Full genome/assembly alignment
446 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 462 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
447 463
448 For cross-species full-genome alignment, the scoring system needs to be 464 For cross-species full-genome alignment, the scoring system needs to be
449 tuned according to the sequence divergence. 465 tuned according to the sequence divergence.
466
467 Self-homology map creation
468 ^^^^^^^^^^^^^^^^^^^^^^^^^^
469
470 A self-homology map is created by mapping a genome (e.g. that of E. coli)
471 against itself. When this option is used the same FASTA file should
472 be used for reference and for the (single ended mode) query.
450 473
451 Advanced features 474 Advanced features
452 ~~~~~~~~~~~~~~~~~ 475 ~~~~~~~~~~~~~~~~~
453 476
454 Working with >65535 CIGAR operations 477 Working with >65535 CIGAR operations