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comparison unicycler.xml @ 2:e92675014ac9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
author iuc
date Tue, 28 Nov 2017 10:53:47 -0500
parents f13d0498a199
children c4eac0c7e542
comparison
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1:f13d0498a199 2:e92675014ac9
1 <tool id="unicycler" name="Create assemblies with Unicycler" version="0.4.1"> 1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.1">
2 <macros>
3 <token name="@VERSION@">0.4.1</token>
4 </macros>
2 <requirements> 5 <requirements>
3 <requirement type="package" version="0.4.1">unicycler</requirement> 6 <requirement type="package" version="@VERSION@">unicycler</requirement>
4 </requirements> 7 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
6 9 ## Preparing files
7 ## Preparing files 10 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
8 11 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
9 #if str( $paired_unpaired.fastq_input_selector ) == "paired": 12 #set fq1 = "fq1.fastq"
10 13 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
11 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'): 14 #set fq1 = "fq1.fastq.gz"
12 ln -s '${paired_unpaired.fastq_input1}' fq1.fastq &&
13 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
14 ln -s '${paired_unpaired.fastq_input1}' fq1.fastq.gz &&
15 #end if
16
17 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger'):
18 ln -s '${paired_unpaired.fastq_input2}' fq2.fastq &&
19 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz'):
20 ln -s '${paired_unpaired.fastq_input1}' fq2.fastq.gz &&
21 #end if
22
23 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection":
24
25 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger'):
26 ln -s '${paired_unpaired.fastq_input1.forward}' fq1.fastq &&
27 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz'):
28 ln -s '${paired_unpaired.fastq_input1.forward}' fq1.fastq.gz &&
29 #end if
30
31 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger'):
32 ln -s '${paired_unpaired.fastq_input1.reverse}' fq2.fastq &&
33 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz'):
34 ln -s '${paired_unpaired.fastq_input2.reverse}' fq2.fastq.gz &&
35 #end if
36
37 #elif str( $paired_unpaired.fastq_input_selector ) == "single":
38
39 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
40 ln -s '${paired_unpaired.fastq_input1}' fq.fastq &&
41 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
42 ln -s '${paired_unpaired.fastq_input1}' fq.fastq.gz &&
43 #end if
44
45 #end if 15 #end if
46 16 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger')
47 ## Get location for pilon installation 17 #set fq2 = "fq2.fastq"
48 18 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz')
49 pilon=`pilon --jar_dir` && 19 #set fq2 = "fq2.fastq.gz"
50
51 #if $long_reads:
52 #if $long_reads.is_of_type('fastqsanger'):
53 #set lr = "lr.fastq"
54 ln -s '${long_reads}' lr.fastq &&
55 #elif $long_reads.is_of_type('fastqsanger.gz'):
56 #set lr = "lr.fastq.gz"
57 ln -s '${long_reads}' lr.fastq.gz &&
58 #elif $long_reads.is_of_type('fasta'):
59 #set lr = "lr.fasta"
60 ln -s '${long_reads}' lr.fasta &&
61 #end if
62 #end if 20 #end if
63 21 ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
64 ## Running Unicycler 22 ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
65 23 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
66 unicycler -t "\${GALAXY_SLOTS:-4}" 24 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger')
67 25 #set fq1 = "fq1.fastq"
68 -o ./ 26 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz')
69 --verbosity 3 27 #set fq1 = "fq1.fastq.gz"
70 --pilon_path \$pilon
71
72 #if str( $paired_unpaired.fastq_input_selector ) != "single":
73
74 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
75 -1 fq1.fastq
76 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
77 -1 fq1.fastq.gz
78 #end if
79
80 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger'):
81 -2 fq2.fastq
82 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz'):
83 -2 fq2.fastq.gz
84 #end if
85
86 #else:
87
88 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
89 -s fq.fastq
90 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
91 -s fq.fastq.gz
92 #end if
93
94 #end if 28 #end if
95 29 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger')
96 #if $long_reads: 30 #set fq2 = "fq2.fastq"
97 31 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz')
98 -l $lr 32 #set fq2 = "fq2.fastq.gz"
99
100 #end if 33 #end if
101 34 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
102 ## General Unicycler Options section 35 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
103 ## ---------------------------------------------------------- 36 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
104 37 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
105 --mode '${uc_opt.mode}' 38 #set fq = "fq.fastq"
106 39 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
107 #if $uc_opt.min_fasta_length: 40 #set fq = "fq.fastq.gz"
108 --min_fasta_length $uc_opt.min_fasta_length
109 #end if 41 #end if
110 42 ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
111 #if $uc_opt.lin_seq: 43 #end if
112 --expected_linear $uc_opt.lin_seq 44 #if $long
45 #if $long.is_of_type('fastqsanger')
46 #set lr = "lr.fastq"
47 #elif $long.is_of_type('fastqsanger.gz')
48 #set lr = "lr.fastq.gz"
49 #elif $long.is_of_type('fasta')
50 #set lr = "lr.fasta"
113 #end if 51 #end if
114 52 ln -s '${long}' '$lr' &&
115 $uc_opt.no_correct 53 #end if
116 $uc_opt.no_rotate 54 ## Get location for pilon installation
117 55 pilon=`pilon --jar_dir` &&
118 ## Rotation Options section 56 ## Running Unicycler
119 ## ---------------------------------------------------------- 57 unicycler -t "\${GALAXY_SLOTS:-4}"
120 58 -o ./
121 #if $spades.min_kmer_frac: 59 --verbosity 3
122 --min_kmer_frac $spades.min_kmer_frac 60 --pilon_path \$pilon
123 #end if 61 #if str( $paired_unpaired.fastq_input_selector ) != "single"
124 62 -1 '$fq1'
125 #if $spades.max_kmer_frac: 63 -2 '$fq2'
126 --max_kmer_frac $spades.max_kmer_frac 64 #else
127 #end if 65 -s '$fq'
128 66 #end if
129 #if $spades.kmer_count: 67 #if $long
130 --kmer_count $spades.kmer_count 68 -l $lr
131 #end if 69 #end if
132 70 ## General Unicycler Options section
133 ## Rotation Options section 71 ## ----------------------------------------------------------
134 ## ---------------------------------------------------------- 72 --mode '$mode'
135 73 --min_fasta_length '$min_fasta_length'
136 #if $rotation.start_genes: 74 --linear_seqs '$linear_seqs'
137 --start_genes '${rotation.rotation_fasta.start_genes}' 75 ## Spades Options section
138 #end if 76 ## ----------------------------------------------------------
139 77 $spades.no_correct
140 #if $rotation.start_gene_id: 78 --min_kmer_frac '$spades.min_kmer_frac'
141 --start_gene_id $rotation.start_gene_id 79 --max_kmer_frac '$spades.max_kmer_frac'
142 #end if 80 --kmer_count '$spades.kmer_count'
143 81 --depth_filter '$spades.depth_filter'
144 #if $rotation.start_gene_cov: 82 ## Rotation Options section
145 --start_gene_cov $rotation.start_gene_cov 83 ## ----------------------------------------------------------
146 #end if 84 $rotation.no_rotate
147 85 #if $rotation.start_genes
148 ## Pilon Options section 86 --start_genes '$rotation.start_genes'
149 ## ---------------------------------------------------------- 87 #end if
150 88 --start_gene_id '$rotation.start_gene_id'
151 #if $pilon.min_polish_size: 89 --start_gene_cov '$rotation.start_gene_cov'
152 --min_polish_size $pilon.min_polish_size 90 ## Pilon Options section
153 #end if 91 ## ----------------------------------------------------------
154 92 $pilon.no_pilon
155 ## Graph Cleaning Options sdection 93 #if str($pilon.min_polish_size) != ''
156 ## ---------------------------------------------------------- 94 --min_polish_size '$pilon.min_polish_size'
157 95 #end if
158 #if $graph_clean.min_component_size: 96 ## Graph cleaning Options sdection
159 --min_component_size $graph_clean.min_component_size 97 ## ----------------------------------------------------------
160 #end if 98 --min_component_size '$graph_clean.min_component_size'
161 #if $graph_clean.min_dead_end_size: 99 --min_dead_end_size '$graph_clean.min_dead_end_size'
162 --min_dead_end_size $graph_clean.min_dead_end_size 100 ## Long Read Alignment Options
163 #end if 101 ## ----------------------------------------------------------
164 102 #if $lr_align.contamination
165 ## Long Read Alignment Options 103 --contamination '$lr_align.contamination'
166 ## ---------------------------------------------------------- 104 #end if
167 105 --scores '${lr_align.scores}'
168 106 #if str($lr_align.low_score) != ''
169 #if $lr_align.contamination_fasta: 107 --low_score '$lr_align.low_score'
170 --contamination '${lr_align.contamination_fasta}' 108 #end if
171 #end if 109 ## Miniasm requires racon, which is not available for python 3.x
172 110 --no_miniasm
173 #if $lr_align.scores:
174 --scores '${lr_align.scores}'
175 #end if
176
177 #if $lr_align.low_score:
178 --low_score $lr_align.low_score
179 #end if
180
181 ## Miniasm requires racon, which is not available for python 3.x
182 --no_miniasm
183
184 ]]></command> 111 ]]></command>
185
186 <inputs> 112 <inputs>
187 <conditional name="paired_unpaired"> 113 <conditional name="paired_unpaired">
188 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data"> 114 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data">
189 <option selected="True" value="paired">Paired</option> 115 <option selected="True" value="paired">Paired</option>
190 <option value="paired_collection">Paired Collection</option> 116 <option value="paired_collection">Paired Collection</option>
199 </when> 125 </when>
200 <when value="single"> 126 <when value="single">
201 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/> 127 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
202 </when> 128 </when>
203 </conditional> 129 </conditional>
204 <param name="long_reads" argument="--long" optional="True" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/> 130 <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/>
205 131 <param argument="--mode" type="select" label="Select Bridging mode">
206 <section name="uc_opt" expanded="True" title="Unicycler options"> 132 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
207 <param argument="--mode" type="select" label="Select Bridging mode"> 133 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
208 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> 134 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
209 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option> 135 </param>
210 <option value="bold">Bold (longest contigs, higher misassembly rate)</option> 136 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/>
211 </param> 137 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/>
212 <param argument="--min_fasta_length" optional="True" type="integer" value="" label="Exclude contigs from the FASTA file which are shorter than this length (bp)" help="default = 1"/> 138 <section name="spades" expanded="False" title="SPAdes options" help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!">
213 <param argument="--no_correct" optional="True" type="boolean" checked="False" truevalue="--no_correct" falsevalue="" label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/> 139 <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue="" label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>
214 <param argument="--no_rotate" optional="True" type="boolean" checked="False" truevalue="--no_rotate" falsevalue="" label="Do not rotate completed replicons to start at a standard gene." help="Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence."/> 140 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2" label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
215 <param argument="--no_pilon" optional="True" type="boolean" checked="False" truevalue="--no_pilon" falsevalue="" label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/> 141 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95" label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
216 <param name="lin_seq" argument="--expected_linear_seqs" optional="True" type="integer" value="" label="The expected number of linear (i.e. non-circular) sequences in the assembly" help="default = 0"/> 142 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/>
143 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/>
217 </section> 144 </section>
218 145 <section name="rotation" expanded="false" title="Rotation options" help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!">
219 <section name="spades" expanded="False" title="SPAdes options" help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!"> 146 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue="" label="Do not rotate completed replicons to start at a standard gene." help="Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence."/>
220 <param argument="--min_kmer_frac" optional="True" type="float" min="0" max="1" value="" label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length" help="default = 0.2"/> 147 <param argument="--start_genes" optional="true" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" />
221 <param argument="--max_kmer_frac" optional="True" type="float" min="0" max="1" value="" label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length" help="default = 0.95"/> 148 <param argument="--start_gene_id" type="float" min="0" max="100" value="90" label="The minimum required BLAST percent identity for a start gene search"/>
222 <param argument="--kmer_count" optional="True" type="integer" value="" label="Number of k-mer steps to use in SPAdes assembly" help="default = 10"/> 149 <param argument="--start_gene_cov" type="float" min="0" max="100" value="95" label="The minimum required BLAST percent coverage for a start gene search"/>
223 </section> 150 </section>
224 151 <section name="pilon" title="Pilon options" expanded="false">
225 <section name="rotation" expanded="False" title="Rotation options" help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!"> 152 <param argument="--no_pilon" type="boolean" checked="false" truevalue="--no_pilon" falsevalue="" label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/>
226 <param argument="--start_genes" optional="True" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" /> 153 <param argument="--min_polish_size" type="integer" min="0" value="1000" label="Contigs shorter than this value (bp) will not be polished using Pilon"/>
227 <param argument="--start_gene_id" optional="True" type="integer" min="0" max="100" value="" label="The minimum required BLAST percent identity for a start gene search" help="default = 90"/>
228 <param argument="--start_gene_cov" optional="True" type="integer" min="0" max="100" value="" label="The minimum required BLAST percent coverage for a start gene search" help="default = 95"/>
229 </section> 154 </section>
230 155 <section name="graph_clean" expanded="false" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete.">
231 <section name="pilon" title="Pilon options" expanded="False"> 156 <param argument="--min_component_size" type="integer" min="0" value="1000" label="Unbridged graph components smaller than this size will be removed from the final graph" />
232 <param argument="--min_polish_size" optional="True" type="integer" min="0" label="Contigs shorter than this value (bp) will not be polished using Pilon" help="default = 1000"/> 157 <param argument="--min_dead_end_size" type="integer" min="0" value="1000" label="Graph dead ends smaller than this size will be removed from the final graph"/>
233 </section> 158 </section>
234 159 <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
235 <section name="graph_clean" expanded="False" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete."> 160 <param argument="--contamination" optional="true" type="data" format="fasta" label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />
236 <param argument="--min_component_size" optional="True" type="integer" value="" label="Unbridged graph components smaller than this size will be removed from the final graph" help="default = 1000"/> 161 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/>
237 <param argument="--min_dead_end_size" optional="True" type="integer" value="" label="Graph dead ends smaller than this size will be removed from the final graph" help="default = 1000"/> 162 <param argument="--low_score" optional="true" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>
238 </section>
239
240 <section name="lr_align" expanded="False" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
241 <param name="contamination_fasta" argument="--contamination" optional="True" type="data" format="fasta" label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />
242 <param argument="--scores" optional="True" type="text" value="" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend" help="default = 3,-6,-5,-2"/>
243 <param argument="--low_score" optional="True" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>
244 </section> 163 </section>
245 </inputs> 164 </inputs>
246
247 <outputs> 165 <outputs>
248 <data format="txt" name="assembly_grapth" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> 166 <data name="assembly_graph" format="txt" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
249 <data format="fasta" name="assembly" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> 167 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
250 </outputs> 168 </outputs>
251
252 <tests> 169 <tests>
253 <test> 170 <test>
254 <param name="fastq_input_selector" value="paired" /> 171 <conditional name="paired_unpaired">
255 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> 172 <param name="fastq_input_selector" value="paired" />
256 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> 173 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
174 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
175 </conditional>
257 <param name="mode" value="normal" /> 176 <param name="mode" value="normal" />
258 <param name="no_correct" value="true" /> 177 <param name="min_fasta_length" value="100"/>
259 <param name="no_rotate" value="false" /> 178 <param name="linear_seqs" value="0"/>
260 <param name="no_pilon" value="false" /> 179 <section name="spades">
261 <output ftype="fasta" name="assembly"> 180 <param name="no_correct" value="true"/>
181 <param name="min_kmer_frac" value="0.2"/>
182 <param name="max_kmer_frac" value="0.95"/>
183 <param name="kmer_count" value="10"/>
184 <param name="depth_filter" value="0.25"/>
185 </section>
186 <section name="rotation">
187 <param name="no_rotate" value=""/>
188 <param name="start_gene_id" value="90"/>
189 <param name="start_gene_cov" value="95"/>
190 </section>
191 <section name="pilon">
192 <param name="no_pilon" value=""/>
193 <param name="min_polish_size" value="1000"/>
194 </section>
195 <section name="graph_clean">
196 <param name="min_component_size" value="1000"/>
197 <param name="min_dead_end_size" value="1000"/>
198 </section>
199 <section name="lr_align">
200 <param name="scores" value="3,-6,-5,-2"/>
201 </section>
202 <output name="assembly_graph" ftype="txt">
203 <assert_contents>
204 <has_text text="TACGGGGAAGGACGTC"/>
205 </assert_contents>
206 </output>
207 <output name="assembly" ftype="fasta">
262 <assert_contents> 208 <assert_contents>
263 <has_text text="length=5386" /> 209 <has_text text="length=5386" />
264 </assert_contents> 210 </assert_contents>
265 </output> 211 </output>
266 </test> 212 </test>
274 This command causes a segfault with the current version of unicycler on bioconda for Linux 220 This command causes a segfault with the current version of unicycler on bioconda for Linux
275 during the minimap step (which seems to be compiled C code). A gist of the log can be found 221 during the minimap step (which seems to be compiled C code). A gist of the log can be found
276 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb. 222 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb.
277 --> 223 -->
278 <test> 224 <test>
279 <param name="fastq_input_selector" value="paired" /> 225 <conditional name="paired_unpaired">
280 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> 226 <param name="fastq_input_selector" value="paired" />
281 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> 227 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" />
282 <param name="long_reads" value="onp.fa" ftype="fasta" /> 228 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" />
229 </conditional>
230 <param name="long" value="onp.fa" ftype="fasta" />
283 <param name="mode" value="normal" /> 231 <param name="mode" value="normal" />
284 <param name="no_correct" value="true" /> 232 <param name="min_fasta_length" value="100"/>
285 <param name="no_rotate" value="false" /> 233 <param name="linear_seqs" value="0"/>
286 <param name="no_pilon" value="false" /> 234 <section name="spades">
287 <output ftype="fasta" name="assembly"> 235 <param name="no_correct" value="true"/>
236 <param name="min_kmer_frac" value="0.2"/>
237 <param name="max_kmer_frac" value="0.95"/>
238 <param name="kmer_count" value="10"/>
239 <param name="depth_filter" value="0.25"/>
240 </section>
241 <section name="rotation">
242 <param name="no_rotate" value=""/>
243 <param name="start_gene_id" value="90"/>
244 <param name="start_gene_cov" value="95"/>
245 </section>
246 <section name="pilon">
247 <param name="no_pilon" value=""/>
248 <param name="min_polish_size" value="1000"/>
249 </section>
250 <section name="graph_clean">
251 <param name="min_component_size" value="1000"/>
252 <param name="min_dead_end_size" value="1000"/>
253 </section>
254 <section name="lr_align">
255 <param name="scores" value="3,-6,-5,-2"/>
256 </section>
257 <output name="assembly_graph" ftype="txt">
258 <assert_contents>
259 <has_text text="TACGGGGAAGGACGTC" />
260 </assert_contents>
261 </output>
262 <output name="assembly" ftype="fasta">
263 <assert_contents>
264 <has_text text="length=5386" />
265 </assert_contents>
266 </output>
267 </test>
268 <test>
269 <conditional name="paired_unpaired">
270 <param name="fastq_input_selector" value="paired_collection"/>
271 <param name="fastq_input1">
272 <collection type="paired">
273 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" />
274 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" />
275 </collection>
276 </param>
277 </conditional>
278 <param name="mode" value="normal" />
279 <param name="min_fasta_length" value="100"/>
280 <param name="linear_seqs" value="0"/>
281 <section name="spades">
282 <param name="no_correct" value="true"/>
283 <param name="min_kmer_frac" value="0.2"/>
284 <param name="max_kmer_frac" value="0.95"/>
285 <param name="kmer_count" value="10"/>
286 <param name="depth_filter" value="0.25"/>
287 </section>
288 <section name="rotation">
289 <param name="no_rotate" value=""/>
290 <param name="start_gene_id" value="90"/>
291 <param name="start_gene_cov" value="95"/>
292 </section>
293 <section name="pilon">
294 <param name="no_pilon" value="true"/>
295 <param name="min_polish_size" value="1000"/>
296 </section>
297 <section name="graph_clean">
298 <param name="min_component_size" value="1000"/>
299 <param name="min_dead_end_size" value="1000"/>
300 </section>
301 <section name="lr_align">
302 <param name="scores" value="3,-6,-5,-2"/>
303 </section>
304 <output name="assembly_graph" ftype="txt">
305 <assert_contents>
306 <has_text text="TACGGGGAAGGACGTC" />
307 </assert_contents>
308 </output>
309 <output name="assembly" ftype="fasta">
288 <assert_contents> 310 <assert_contents>
289 <has_text text="length=5386" /> 311 <has_text text="length=5386" />
290 </assert_contents> 312 </assert_contents>
291 </output> 313 </output>
292 </test> 314 </test>
388 410
389 **Expected number of linear sequences** 411 **Expected number of linear sequences**
390 412
391 If you expect your sample to contain linear (non circular) sequences, set this option:: 413 If you expect your sample to contain linear (non circular) sequences, set this option::
392 414
393 --expected_linear_seqs EXPECTED_LINEAR_SEQS 415 --linear_seqs EXPECTED_LINEAR_SEQS
394 The expected number of linear (i.e. non-circular) 416 The expected number of linear (i.e. non-circular)
395 sequences in the underlying sequence 417 sequences in the underlying sequence
396 418
397 ---- 419 ----
398 420
409 expressed as a fraction of the read length 431 expressed as a fraction of the read length
410 (default: 0.95) 432 (default: 0.95)
411 --kmer_count KMER_COUNT 433 --kmer_count KMER_COUNT
412 Number of k-mer steps to use in 434 Number of k-mer steps to use in
413 SPAdes assembly (default: 10) 435 SPAdes assembly (default: 10)
436 --depth_filter DEPTH_FILTER
437 Filter out contigs lower than this fraction
438 of the chromosomal depth, if doing so does
439 not result in graph dead ends (default: 0.25)
414 440
415 ---- 441 ----
416 442
417 **Rotation options** 443 **Rotation options**
418 444