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comparison hifiasm.xml @ 3:9ef6920c3089 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
author bgruening
date Thu, 24 Jun 2021 19:42:15 +0000
parents f3c89da3af16
children 3f7be05a1597
comparison
equal deleted inserted replaced
2:f3c89da3af16 3:9ef6920c3089
1 <tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0"> 1 <tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0">
2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description> 2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.15.3</token> 4 <token name="@VERSION@">0.15.4</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@" multiple="true" label="Input reads" /> 7 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
8 </xml> 8 </xml>
9 </macros> 9 </macros>
96 --n-perturb $hic_partition.n_perturb 96 --n-perturb $hic_partition.n_perturb
97 #end if 97 #end if
98 #if $hic_partition.f_perturb: 98 #if $hic_partition.f_perturb:
99 --f-perturb $hic_partition.f_perturb 99 --f-perturb $hic_partition.f_perturb
100 #end if 100 #end if
101 --l-msjoin $hic_partition.l_msjoin
101 #end if 102 #end if
102 103
103 ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly. 104 ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly.
104 --primary 105 --primary
105 $input_filenames 106 $input_filenames
106 107 #if $log_out:
108 2> output.log
109 #end if
107 ]]> 110 ]]>
108 </command> 111 </command>
109 <inputs> 112 <inputs>
110 <conditional name="mode"> 113 <conditional name="mode">
111 <param name="mode_selector" type="select" label="Assembly mode"> 114 <param name="mode_selector" type="select" label="Assembly mode">
123 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" /> 126 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
124 <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" /> 127 <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />
125 </when> 128 </when>
126 </conditional> 129 </conditional>
127 <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" /> 130 <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" />
128
129 <conditional name="advanced_options"> 131 <conditional name="advanced_options">
130 <param name="advanced_selector" type="select" label="Advanced options"> 132 <param name="advanced_selector" type="select" label="Advanced options">
131 <option value="blank">Leave default</option> 133 <option value="blank">Leave default</option>
132 <option value="set">Specify</option> 134 <option value="set">Specify</option>
133 </param> 135 </param>
192 <param argument="--h2" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R2 reads" /> 194 <param argument="--h2" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R2 reads" />
193 <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed" /> 195 <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed" />
194 <param argument="--n-weight" type="integer" min="1" value="" optional="true" label="Rounds of reweighting Hi-C links" /> 196 <param argument="--n-weight" type="integer" min="1" value="" optional="true" label="Rounds of reweighting Hi-C links" />
195 <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation" /> 197 <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation" />
196 <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation" /> 198 <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation" />
197 </when> 199 <param argument="--l-msjoin" type="integer" min="0" value="500000" label="Detect misjoined unitigs of greater than or equal to specified size" help="A value of 0 disables this filter"/>
200 </when>
198 </conditional> 201 </conditional>
199 202 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
200 </inputs> 203 </inputs>
201 <outputs> 204 <outputs>
202 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph"> 205 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph">
203 <filter>mode['mode_selector'] == 'standard'</filter> 206 <filter>mode['mode_selector'] == 'standard'</filter>
204 </data> 207 </data>
228 <filter>hic_partition['hic_partition_selector'] == 'set'</filter> 231 <filter>hic_partition['hic_partition_selector'] == 'set'</filter>
229 </data> 232 </data>
230 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.bp.hap2.p_ctg.gfa" label="${tool.name} ${on_string}, HI-C hap2 balanced contig graph hap2"> 233 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.bp.hap2.p_ctg.gfa" label="${tool.name} ${on_string}, HI-C hap2 balanced contig graph hap2">
231 <filter>hic_partition['hic_partition_selector'] == 'set'</filter> 234 <filter>hic_partition['hic_partition_selector'] == 'set'</filter>
232 </data> 235 </data>
236 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}, log file">
237 <filter>log_out</filter>
238 </data>
233 </outputs> 239 </outputs>
234 <tests> 240 <tests>
235 <test> 241 <test>
236 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 242 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
237 <param name="filter_bits" value="0" /> 243 <param name="filter_bits" value="0" />
256 <assert_contents> 262 <assert_contents>
257 <has_size value="0"/> 263 <has_size value="0"/>
258 </assert_contents> 264 </assert_contents>
259 </output> 265 </output>
260 </test> 266 </test>
267 <!-- Test logfile out-->
268 <test>
269 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
270 <param name="filter_bits" value="0" />
271 <param name="mode_selector" value="standard" />
272 <param name="log_out" value="yes"/>
273 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
274 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
275 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
276 <output name="alternate_contig_graph" ftype="gfa1">
277 <assert_contents>
278 <has_size value="0"/>
279 </assert_contents>
280 </output>
281 <output name="log_file" ftype="txt">
282 <assert_contents>
283 <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/>
284 </assert_contents>
285 </output>
286 </test>
261 287
262 <!-- Test Hi-C 288 <!-- Test Hi-C
263 <test> 289 <test>
264 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 290 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
265 <param name="filter_bits" value="0" /> 291 <param name="filter_bits" value="0" />
266 <param name="mode_selector" value="standard" /> 292 <param name="mode_selector" value="standard" />
267 <conditional name="hic_partition"> 293 <conditional name="hic_partition">
268 <param name="hic_partition_selector" value="set"/> 294 <param name="hic_partition_selector" value="set"/>