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comparison hifiasm.xml @ 6:5bec28269d95 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"
author bgruening
date Sat, 12 Feb 2022 17:15:48 +0000
parents 045c7c3d8e59
children 366a11d316a7
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5:045c7c3d8e59 6:5bec28269d95
1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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="@TOOL_VERSION@">0.16.1</token> 4 <token name="@TOOL_VERSION@">0.16.1</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> 6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
7 <xml name="reads"> 7 <xml name="reads">
8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" /> 8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
9 </xml> 9 </xml>
10 </macros> 10 </macros>
218 <param name="drop_kmers" argument="-D" type="float" value="5.0" label="Drop k-mers" help="K-mers that occur more than this value multiplied by the coverage will be discarded" /> 218 <param name="drop_kmers" argument="-D" type="float" value="5.0" label="Drop k-mers" help="K-mers that occur more than this value multiplied by the coverage will be discarded" />
219 <param name="max_overlaps" argument="-N" type="integer" value="100" label="Maximum overlaps to consider" help="The software selects the larger of this value and the k-mer count multiplied by coverage" /> 219 <param name="max_overlaps" argument="-N" type="integer" value="100" label="Maximum overlaps to consider" help="The software selects the larger of this value and the k-mer count multiplied by coverage" />
220 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" /> 220 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" />
221 <param argument="--min-hist-cnt" type="integer" min="0" value="" optional="true" label="Minimum count threshold" help="When analyzing the k-mer spectrum, ignore counts below this value" /> 221 <param argument="--min-hist-cnt" type="integer" min="0" value="" optional="true" label="Minimum count threshold" help="When analyzing the k-mer spectrum, ignore counts below this value" />
222 <param argument="--max-kocc" type="integer" min="0" value="20000" label="Maximum k-mer ocurrence" help="Employ k-mers occurring less than INT times to rescue repetitive overlaps" /> 222 <param argument="--max-kocc" type="integer" min="0" value="20000" label="Maximum k-mer ocurrence" help="Employ k-mers occurring less than INT times to rescue repetitive overlaps" />
223 <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size" help="Estimated haploid genome size used for inferring read coverage. If not provided, this parameter will be infered by hifism. Common suffices are required, for example, 100m or 3g"> 223 <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size"
224 help="Estimated haploid genome size used for inferring read coverage. If not provided, this parameter will be infered by hifism. Common suffices are required, for example, 100m or 3g">
224 <sanitizer invalid_char=""> 225 <sanitizer invalid_char="">
225 <valid initial="string.digits"> 226 <valid initial="string.digits">
226 <add value="k" /> 227 <add value="k" />
227 <add value="K" /> 228 <add value="K" />
228 <add value="m" /> 229 <add value="m" />
269 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 270 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
270 </data> 271 </data>
271 <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph"> 272 <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph">
272 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 273 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
273 </data> 274 </data>
274 <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.bp.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1"> 275 <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
275 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 276 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
276 </data> 277 </data>
277 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.bp.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2"> 278 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
278 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 279 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
279 </data> 280 </data>
280 <!--Trio outputs with Hi-c reads--> 281 <!--Trio outputs with Hi-c reads-->
281 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph"> 282 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph">
282 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter> 283 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
352 </conditional> 353 </conditional>
353 <output name="hic_pcontig_graph" file="hifiasm-out-hifi-p.gfa" ftype="gfa1" /> 354 <output name="hic_pcontig_graph" file="hifiasm-out-hifi-p.gfa" ftype="gfa1" />
354 <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" /> 355 <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" />
355 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1"> 356 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1">
356 <assert_contents> 357 <assert_contents>
357 <has_size value="0"/> 358 <has_text_matching expression="^S" />
359 <has_size value="59529" delta="500"/>
358 </assert_contents> 360 </assert_contents>
359 </output> 361 </output>
360 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" > 362 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" >
361 <assert_contents> 363 <assert_contents>
362 <has_size value="0"/> 364 <has_text_matching expression="^S" />
365 <has_size value="59529" delta="500"/>
363 </assert_contents> 366 </assert_contents>
364 </output> 367 </output>
365 </test> 368 </test>
366 <!-- Test trio mode --> 369 <!-- Test trio mode -->
367 <test expect_num_outputs="4"> 370 <test expect_num_outputs="4">