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comparison hifiasm.xml @ 7:366a11d316a7 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4
author bgruening
date Tue, 31 May 2022 14:15:45 +0000
parents 5bec28269d95
children 5f625c63b8bc
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6:5bec28269d95 7:366a11d316a7
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@">2</token> 5 <token name="@VERSION_SUFFIX@">3</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>
276 <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>
277 </data> 277 </data>
278 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2"> 278 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
279 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 279 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
280 </data> 280 </data>
281 <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig">
282 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
283 </data>
281 <!--Trio outputs with Hi-c reads--> 284 <!--Trio outputs with Hi-c reads-->
282 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph"> 285 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph">
283 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter> 286 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
284 </data> 287 </data>
285 <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed initig graph"> 288 <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed initig graph">
336 <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/> 339 <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/>
337 </assert_contents> 340 </assert_contents>
338 </output> 341 </output>
339 </test> 342 </test>
340 <!--Test Hi-C reads--> 343 <!--Test Hi-C reads-->
341 <test expect_num_outputs="4"> 344 <test expect_num_outputs="5">
342 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 345 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
343 <param name="filter_bits" value="0" /> 346 <param name="filter_bits" value="0" />
344 <param name="mode_selector" value="standard" /> 347 <param name="mode_selector" value="standard" />
345 <conditional name="hic_partition"> 348 <conditional name="hic_partition">
346 <param name="hic_partition_selector" value="set"/> 349 <param name="hic_partition_selector" value="set"/>
363 <assert_contents> 366 <assert_contents>
364 <has_text_matching expression="^S" /> 367 <has_text_matching expression="^S" />
365 <has_size value="59529" delta="500"/> 368 <has_size value="59529" delta="500"/>
366 </assert_contents> 369 </assert_contents>
367 </output> 370 </output>
371 <output name="hic_raw_initig" ftype="gfa1" >
372 <assert_contents>
373 <has_text_matching expression="^S" />
374 <has_size value="59522" delta="500"/>
375 </assert_contents>
376 </output>
368 </test> 377 </test>
369 <!-- Test trio mode --> 378 <!-- Test trio mode -->
370 <test expect_num_outputs="4"> 379 <test expect_num_outputs="4">
371 <param name="filter_bits" value="0"/> 380 <param name="filter_bits" value="0"/>
372 <conditional name="mode"> 381 <conditional name="mode">