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comparison hifiasm.xml @ 1:6505bd37670d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
author bgruening
date Wed, 03 Mar 2021 16:16:42 +0000
parents bf0a4667e3ce
children f3c89da3af16
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0:bf0a4667e3ce 1:6505bd37670d
1 <tool id="hifiasm" name="Hifiasm" version="@VERSION@"> 1 <tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0">
2 <description>de novo assembler</description> 2 <description>de novo assembler</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.14</token> 4 <token name="@VERSION@">0.14</token>
5 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> 5 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
6 <xml name="reads"> 6 <xml name="reads">
7 <param name="reads" type="data" format="@FORMATS@" label="Input reads" /> 7 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
8 </xml> 8 </xml>
9 </macros> 9 </macros>
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@VERSION@">hifiasm</requirement> 11 <requirement type="package" version="@VERSION@">hifiasm</requirement>
12 <requirement type="package" version="0.1">yak</requirement> 12 <requirement type="package" version="0.1">yak</requirement>
13 </requirements> 13 </requirements>
14 <version_command>hifiasm --version</version_command> 14 <version_command>hifiasm --version</version_command>
15 <command detect_errors="exit_code"> 15 <command detect_errors="exit_code">
16 <![CDATA[ 16 <![CDATA[
17 #if str($mode.mode_selector) == 'standard': 17 #set $input_files = list()
18 ln -s '$mode.reads' input.${mode.reads.extension} && 18 #set $hap1_inputs = list()
19 #else: 19 #set $hap2_inputs = list()
20 ln -s '$mode.hap1_reads' hap1_reads.${mode.hap1_reads.extension} && 20 #for idx, read in enumerate($mode.reads):
21 ln -s '$mode.hap2_reads' hap2_reads.${mode.hap2_reads.extension} && 21 #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension)
22 yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap1.yak hap1_reads.${mode.hap1_reads.extension} && 22 ln -s '$read' $inputfile &&
23 yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap2.yak hap2_reads.${mode.hap2_reads.extension} && 23 $input_files.append($inputfile)
24 #end if 24 #end for
25 hifiasm -i input.${mode.reads.extension} -t \${GALAXY_SLOTS:-1} -o output -f $filter_bits 25 #set $input_filenames = ' '.join($input_files)
26 #if str($mode.mode_selector) == 'trio':
27 #for idx, read in enumerate($mode.hap1_reads):
28 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
29 ln -s '$read' $inputfile &&
30 $hap1_inputs.append($inputfile)
31 #end for
32 #for idx, read in enumerate($mode.hap2_reads):
33 #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
34 ln -s '$read' $inputfile &&
35 $hap2_inputs.append($inputfile)
36 #end for
37 #set $hap1_filenames = ' '.join($hap1_inputs)
38 #set $hap2_filenames = ' '.join($hap2_inputs)
39 yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
40 yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
41 #end if
42 hifiasm -i $input_filenames -t \${GALAXY_SLOTS:-1} -o output -f $filter_bits
43 #if str($mode.mode_selector) == 'trio':
44 -1 hap1.yak -2 hap2.yak
45 #end if
26 #if str($advanced_options.advanced_selector) == 'set': 46 #if str($advanced_options.advanced_selector) == 'set':
27 -z $advanced_options.adapter_length 47 -z $advanced_options.adapter_length
28 -k $advanced_options.kmer_length 48 -k $advanced_options.kmer_length
29 -w $advanced_options.window_size 49 -w $advanced_options.window_size
30 -D $advanced_options.drop_kmers 50 -D $advanced_options.drop_kmers
37 -p $assembly_options.pop_unitigs 57 -p $assembly_options.pop_unitigs
38 -n $assembly_options.remove_tips 58 -n $assembly_options.remove_tips
39 -x $assembly_options.max_overlap 59 -x $assembly_options.max_overlap
40 -y $assembly_options.min_overlap 60 -y $assembly_options.min_overlap
41 $assembly_options.disable_post_join 61 $assembly_options.disable_post_join
42 --pb-range $assembly_options.pb_range
43 #end if 62 #end if
44 #if str($mode.mode_selector) == 'trio': 63 #if str($mode.mode_selector) == 'trio':
45 -1 hap1.yak 64 -1 hap1.yak
46 -2 hap2.yak 65 -2 hap2.yak
47 -c $mode.max_kmers 66 -c $mode.max_kmers
67 <when value="standard"> 86 <when value="standard">
68 <expand macro="reads" /> 87 <expand macro="reads" />
69 </when> 88 </when>
70 <when value="trio"> 89 <when value="trio">
71 <expand macro="reads" /> 90 <expand macro="reads" />
72 <param name="hap1_reads" type="data" format="fastq,fastq.gz" label="Haplotype 1 reads" /> 91 <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />
73 <param name="hap2_reads" type="data" format="fastq,fastq.gz" label="Haplotype 2 reads" /> 92 <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />
74 <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" /> 93 <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" />
75 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" /> 94 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
76 </when> 95 </when>
77 </conditional> 96 </conditional>
78 <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter" /> 97 <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter" />
103 <param name="pop_unitigs" argument="-p" type="integer" value="100000" label="Minimum unitig bubble size" help="Pop unitig graph bubbles smaller than this value" /> 122 <param name="pop_unitigs" argument="-p" type="integer" value="100000" label="Minimum unitig bubble size" help="Pop unitig graph bubbles smaller than this value" />
104 <param name="remove_tips" argument="-n" type="integer" value="3" label="Tip unitigs" help="Keep only tip unitigs with a number of reads greater than or equal to this value" /> 123 <param name="remove_tips" argument="-n" type="integer" value="3" label="Tip unitigs" help="Keep only tip unitigs with a number of reads greater than or equal to this value" />
105 <param name="max_overlap" argument="-x" type="float" min="0" max="1" value="0.8" label="Maximum overlap drop ratio" /> 124 <param name="max_overlap" argument="-x" type="float" min="0" max="1" value="0.8" label="Maximum overlap drop ratio" />
106 <param name="min_overlap" argument="-y" type="float" min="0" max="1" value="0.2" label="Minimum overlap drop ratio" /> 125 <param name="min_overlap" argument="-y" type="float" min="0" max="1" value="0.2" label="Minimum overlap drop ratio" />
107 <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" /> 126 <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" />
108 <param argument="--pb-range" type="integer" min="0" max="100" value="0" label="Inconsistent contigs" help="If this option is set to a value greater than zero the tool generates an additional BED dataset containing regions that are &gt;= x% inconsistent." />
109 </when> 127 </when>
110 </conditional> 128 </conditional>
111 <conditional name="purge_options"> 129 <conditional name="purge_options">
112 <param name="purge_selector" type="select" label="Options for purging duplicates"> 130 <param name="purge_selector" type="select" label="Options for purging duplicates">
113 <option value="blank">Leave default</option> 131 <option value="blank">Leave default</option>
126 <param argument="--high-het" type="boolean" truevalue="--high-het" falsevalue="" label="Experimental high-heterozygosity mode" help="NB: May be unstable" /> 144 <param argument="--high-het" type="boolean" truevalue="--high-het" falsevalue="" label="Experimental high-heterozygosity mode" help="NB: May be unstable" />
127 </when> 145 </when>
128 </conditional> 146 </conditional>
129 </inputs> 147 </inputs>
130 <outputs> 148 <outputs>
131 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string} Haplotype-resolved raw unitig graph"> 149 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph">
132 <filter>mode['mode_selector'] == 'standard'</filter> 150 <filter>mode['mode_selector'] == 'standard'</filter>
133 </data> 151 </data>
134 <data name="raw_unitigs" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string} Haplotype-resolved raw unitig graph"> 152 <data name="raw_unitigs" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph">
135 <filter>mode['mode_selector'] == 'trio'</filter> 153 <filter>mode['mode_selector'] == 'trio'</filter>
136 </data> 154 </data>
137 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string} Processed unitig graph"> 155 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}, processed unitig graph">
138 <filter>mode['mode_selector'] == 'standard'</filter> 156 <filter>mode['mode_selector'] == 'standard'</filter>
139 </data> 157 </data>
140 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string} Primary assembly contig graph"> 158 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}, primary assembly contig graph">
141 <filter>mode['mode_selector'] == 'standard'</filter> 159 <filter>mode['mode_selector'] == 'standard'</filter>
142 </data> 160 </data>
143 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string} Alternate assembly contig graph"> 161 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}, alternate assembly contig graph">
144 <filter>mode['mode_selector'] == 'standard'</filter> 162 <filter>mode['mode_selector'] == 'standard'</filter>
145 </data> 163 </data>
146 <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} ${mode.hap1_reads.name} contig graph"> 164 <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} ${mode.hap1_reads.name}, contig graph">
147 <filter>mode['mode_selector'] == 'trio'</filter> 165 <filter>mode['mode_selector'] == 'trio'</filter>
148 </data> 166 </data>
149 <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} ${mode.hap2_reads.name} contig graph"> 167 <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} ${mode.hap2_reads.name}, contig graph">
150 <filter>mode['mode_selector'] == 'trio'</filter> 168 <filter>mode['mode_selector'] == 'trio'</filter>
151 </data> 169 </data>
152 </outputs> 170 </outputs>
153 <tests> 171 <tests>
154 <test> 172 <test>
158 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" /> 176 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
159 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" /> 177 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
160 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" /> 178 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
161 <output name="alternate_contig_graph" file="hifiasm-out1-alternate.gfa" ftype="gfa1" /> 179 <output name="alternate_contig_graph" file="hifiasm-out1-alternate.gfa" ftype="gfa1" />
162 </test> 180 </test>
181 <test>
182 <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" />
183 <param name="filter_bits" value="0" />
184 <param name="mode_selector" value="standard" />
185 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" />
186 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" />
187 <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" />
188 <output name="alternate_contig_graph" file="hifiasm-out2-alternate.gfa" ftype="gfa1" />
189 </test>
163 </tests> 190 </tests>
164 <help><![CDATA[ 191 <help><![CDATA[
165 *********************************** 192 ***********************************
166 HiFiASM - a fast de novo assembler 193 HiFiASM - a fast de novo assembler
167 *********************************** 194 ***********************************
194 - *Minimum unitig bubble* size Pop unitig graph bubbles smaller than this value 221 - *Minimum unitig bubble* size Pop unitig graph bubbles smaller than this value
195 - *Tip unitigs* Keep only tip unitigs with a number of reads greater than or equal to this value 222 - *Tip unitigs* Keep only tip unitigs with a number of reads greater than or equal to this value
196 - *Maximum overlap drop ratio* 223 - *Maximum overlap drop ratio*
197 - *Minimum overlap drop ratio* 224 - *Minimum overlap drop ratio*
198 - *Skip post join contigs step* disable post join contigs step which may improve N50 225 - *Skip post join contigs step* disable post join contigs step which may improve N50
199 - *Inconsistent contigs* If this option is set to a value greater than zero the tool generates an additional BED dataset containing regions that are &gt;= x% inconsistent.
200 226
201 #### Options for purging duplicates 227 #### Options for purging duplicates
202 - *Purge level* 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip] 228 - *Purge level* 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip]
203 - *Similarity threshold for duplicate haplotigs* 229 - *Similarity threshold for duplicate haplotigs*
204 - *Minimum overlapped reads for duplicate haplotigs* 230 - *Minimum overlapped reads for duplicate haplotigs*