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comparison minimap2.xml @ 12:440100db1333 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad
author iuc
date Fri, 31 Aug 2018 07:44:00 -0400
parents 5c73cef26bbe
children ba69511b9e66
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11:5c73cef26bbe 12:440100db1333
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="minimap2" name="Map with minimap2" version="2.5+gx1" profile="17.01"> 2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@" 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>
5 <token name="@TOOL_VERSION@">2.12</token>
6 </macros>
4 <requirements> 7 <requirements>
5 <requirement type="package" version="2.5">minimap2</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>
6 <requirement type="package" version="1.6">samtools</requirement> 9 <requirement type="package" version="1.9">samtools</requirement>
7 </requirements> 10 </requirements>
8 <version_command>minimap2 --version</version_command> 11 <version_command>minimap2 --version</version_command>
9 <command> 12 <command>
10 <![CDATA[ 13 <![CDATA[
11 #if $reference_source.reference_source_selector == 'history': 14 #if $reference_source.reference_source_selector == 'history':
14 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && 17 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
15 #end if 18 #end if
16 minimap2 19 minimap2
17 -x $analysis_type_selector 20 -x $analysis_type_selector
18 ## indexing options 21 ## indexing options
22 $indexing_options.H
19 #if $indexing_options.k: 23 #if $indexing_options.k:
20 -k $indexing_options.k 24 -k $indexing_options.k
21 #end if 25 #end if
22 #if $indexing_options.w: 26 #if $indexing_options.w:
23 -w $indexing_options.w 27 -w $indexing_options.w
26 -I $indexing_options.I 30 -I $indexing_options.I
27 #end if 31 #end if
28 ## Mapping options 32 ## Mapping options
29 #if $mapping_options.f: 33 #if $mapping_options.f:
30 -f $mapping_options.f 34 -f $mapping_options.f
35 #end if
36 #if $mapping_options.min_occ_floor:
37 --min-occ-floor $min_occ_floor
31 #end if 38 #end if
32 #if $mapping_options.g: 39 #if $mapping_options.g:
33 -g $mapping_options.g 40 -g $mapping_options.g
34 #end if 41 #end if
35 #if $mapping_options.G: 42 #if $mapping_options.G:
111 #else if $io_options.output_format == 'CRAM': 118 #else if $io_options.output_format == 'CRAM':
112 -a 119 -a
113 | samtools sort 120 | samtools sort
114 -@\${GALAXY_SLOTS:-2} 121 -@\${GALAXY_SLOTS:-2}
115 -O $io_options.output_format 122 -O $io_options.output_format
123 $io_options.eqx
116 --reference reference.fa 124 --reference reference.fa
117 --output-fmt-option no_ref 125 --output-fmt-option no_ref
118 -o '$alignment_output' 126 -o '$alignment_output'
119 #end if 127 #end if
120 > '$alignment_output' 128 > '$alignment_output'
138 <when value="history"> 146 <when value="history">
139 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" /> 147 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
140 </when> 148 </when>
141 </conditional> 149 </conditional>
142 <section name="indexing_options" title="Indexing options"> 150 <section name="indexing_options" title="Indexing options">
143 <!-- Homopolymer setting seems to not properly overwrite sr preset
144 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/> 151 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
145 -->
146 <param argument="-k" type="integer" min="4" max="28" optional="true" label="k-mer size" help=""/> 152 <param argument="-k" type="integer" min="4" max="28" optional="true" label="k-mer size" help=""/>
147 <param argument="-w" type="integer" min="1" optional="true" label="minimizer window size" help=""/> 153 <param argument="-w" type="integer" min="1" optional="true" label="minimizer window size" help=""/>
148 <param argument="-I" type="integer" min="1" optional="true" label="split index for every N input gigabases" help=""/> 154 <param argument="-I" type="integer" min="1" optional="true" label="split index for every N input gigabases" help=""/>
149 </section> 155 </section>
150 <!-- start unchanged copy from bwa-mem --> 156 <!-- start unchanged copy from bwa-mem -->
169 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> 175 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
170 </when> 176 </when>
171 </conditional> 177 </conditional>
172 <!-- end unchanged copy from bwa-mem --> 178 <!-- end unchanged copy from bwa-mem -->
173 <param name="analysis_type_selector" type="select" label="Select analysis mode (sets default)"> 179 <param name="analysis_type_selector" type="select" label="Select analysis mode (sets default)">
174 <option value="map-pb">-Hk19 (PacBio vs reference mapping)</option> 180 <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19)</option>
175 <option value="map-ont">-k15 (Oxford Nanopore vs reference mapping)</option> 181 <option value="map-ont">Oxford Nanopore read to reference mapping. Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode.</option>
176 <option value="asm5">-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5% div.)</option> 182 <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25)</option>
177 <option value="asm10">-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10% div.)</option> 183 <option value="ava-ont">Oxford Nanopore all-vs-all overlap mapping (-k15 -Xw5 -m100 -g10000 -r2000 --max-chain-skip 25). Similarly, the major difference from ava-pb is that this preset is not using HPC minimizers.</option>
178 <option value="ava-pb">-Hk19 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (PacBio read overlap)</option> 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>
179 <option value="ava-ont">-k15 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (ONT read overlap)</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>
180 <option value="splice">long-read spliced alignment</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>
181 <option value="sr">short single-end reads without splicing</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>
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>
182 </param> 189 </param>
183 <section name="mapping_options" title="Set advanced mapping options" help="Sets -f, -g, -G, -F, -r, -n, -m, -X, -p and -N options." expanded="False"> 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">
184 <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/> 191 <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" />
185 <param argument="-g" type="integer" value="" optional="true" label="stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/> 193 <param argument="-g" type="integer" value="" optional="true" label="stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/>
186 <param argument="-G" type="integer" value="" optional="true" label="max intron length in thousand (effective with -xsplice; changing -r)" help="default=200"/> 194 <param argument="-G" type="integer" value="" optional="true" label="max intron length in thousand (effective with -xsplice; changing -r)" help="default=200"/>
187 <param argument="-F" type="integer" value="" optional="true" label="max fragment length (effective with -xsr or in the fragment mode)" help="default=800" /> 195 <param argument="-F" type="integer" value="" optional="true" label="max fragment length (effective with -xsr or in the fragment mode)" help="default=800" />
188 <param argument="-r" type="integer" value="" optional="true" label="bandwidth used in chaining and DP-based alignment" help="default=500" /> 196 <param argument="-r" type="integer" value="" optional="true" label="bandwidth used in chaining and DP-based alignment" help="default=500" />
189 <param argument="-n" type="integer" value="" optional="true" label="minimal number of minimizers on a chain" help="default=3"/> 197 <param argument="-n" type="integer" value="" optional="true" label="minimal number of minimizers on a chain" help="default=3"/>
219 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below."> 227 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below.">
220 <option value="none">no</option> 228 <option value="none">no</option>
221 <option value="short">short</option> 229 <option value="short">short</option>
222 <option value="long">long</option> 230 <option value="long">long</option>
223 </param> 231 </param>
232 <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="write =/X CIGAR operators"/>
224 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/> 233 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/>
225 </section> 234 </section>
226 </inputs> 235 </inputs>
227 <outputs> 236 <outputs>
228 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)"> 237 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)">