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comparison hifiasm.xml @ 11:cd7936c5a9a5 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
author bgruening
date Thu, 23 Feb 2023 22:34:21 +0000
parents 2061fb3b81b4
children da9d8bf98802
comparison
equal deleted inserted replaced
10:2061fb3b81b4 11:cd7936c5a9a5
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@">0.18.5</token> 4 <token name="@TOOL_VERSION@">0.18.8</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">0</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>
115 --n-hap $purge_options.n_hap 115 --n-hap $purge_options.n_hap
116 #end if 116 #end if
117 #end if 117 #end if
118 118
119 #if str($hic_partition.hic_partition_selector) == 'set': 119 #if str($hic_partition.hic_partition_selector) == 'set':
120 --h1 ${ ' '.join(["'%s'" % $x for $x in $hic1_inputs]) } 120 --h1 ${ ','.join(["'%s'" % $x for $x in $hic1_inputs]) }
121 --h2 ${ ' '.join(["'%s'" % $x for $x in $hic2_inputs]) } 121 --h2 ${ ','.join(["'%s'" % $x for $x in $hic2_inputs]) }
122 #if $hic_partition.seed: 122 #if $hic_partition.seed:
123 --seed $hic_partition.seed 123 --seed $hic_partition.seed
124 #end if 124 #end if
125 #if $hic_partition.n_weight: 125 #if $hic_partition.n_weight:
126 --n-weight $hic_partition.n_weight 126 --n-weight $hic_partition.n_weight
133 #end if 133 #end if
134 --l-msjoin $hic_partition.l_msjoin 134 --l-msjoin $hic_partition.l_msjoin
135 #end if 135 #end if
136 136
137 #if str($ont_integration.ont_integration_selector) == 'set': 137 #if str($ont_integration.ont_integration_selector) == 'set':
138 --ul ${ ' '.join(["'%s'" % $x for $x in $ultralong_inputs]) } 138 --ul ${ ','.join(["'%s'" % $x for $x in $ultralong_inputs]) }
139 #if $ont_integration.ul_rate: 139 #if $ont_integration.ul_rate:
140 --ul-rate $ont_integration.ul_rate 140 --ul-rate $ont_integration.ul_rate
141 #end if 141 #end if
142 #if $ont_integration.ul_tip: 142 #if $ont_integration.ul_tip:
143 --ul-tip $ont_integration.ul_tip 143 --ul-tip $ont_integration.ul_tip
270 </conditional> 270 </conditional>
271 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/> 271 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
272 </inputs> 272 </inputs>
273 <outputs> 273 <outputs>
274 <!--Standard mode--> 274 <!--Standard mode-->
275 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph"> 275 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for pseudohaplotype assembly">
276 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> 276 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
277 </data> 277 </data>
278 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph"> 278 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph for pseudohaplotype assembly">
279 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> 279 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
280 </data> 280 </data>
281 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph"> 281 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph for pseudohaplotype assembly">
282 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> 282 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
283 </data> 283 </data>
284 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph"> 284 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph for pseudohaplotype assembly">
285 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> 285 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
286 </data> 286 </data>
287 <!--Trio outputs without Hi-c reads--> 287 <!--Trio outputs without Hi-c reads-->
288 <data name="hap1_contigs" format="gfa1" from_work_dir="output.dip.hap1.p_ctg.gfa" label="${tool.name} on ${on_string}: hap1.p_ctg contig graph"> 288 <data name="hap1_contigs" format="gfa1" from_work_dir="output.dip.hap1.p_ctg.gfa" label="${tool.name} on ${on_string}: hap1.p_ctg contig graph">
289 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter> 289 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
290 </data> 290 </data>
291 <data name="hap2_contigs" format="gfa1" from_work_dir="output.dip.hap2.p_ctg.gfa" label="${tool.name} on ${on_string}: hap2.p_ctg contig graph"> 291 <data name="hap2_contigs" format="gfa1" from_work_dir="output.dip.hap2.p_ctg.gfa" label="${tool.name} on ${on_string}: hap2.p_ctg contig graph">
292 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter> 292 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
293 </data> 293 </data>
294 <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph"> 294 <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for HiC-phased assembly">
295 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter> 295 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
296 </data> 296 </data>
297 <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph"> 297 <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph for HiC-phased assembly">
298 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter> 298 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
299 </data> 299 </data>
300 <!-- Stardand mode with Hi-C partition outputs --> 300 <!-- Stardand mode with Hi-C partition outputs -->
301 <data name="hic_pcontig_graph" format="gfa1" from_work_dir="output.hic.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C primary contig graph"> 301 <data name="hic_pcontig_graph" format="gfa1" from_work_dir="output.hic.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C primary contig graph">
302 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 302 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
312 </data> 312 </data>
313 <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig"> 313 <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig">
314 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 314 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
315 </data> 315 </data>
316 <!--Trio outputs with Hi-c reads--> 316 <!--Trio outputs with Hi-c reads-->
317 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph"> 317 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw unitig graph">
318 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter> 318 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
319 </data> 319 </data>
320 <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed initig graph"> 320 <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed unitig graph">
321 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter> 321 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
322 </data> 322 </data>
323 <!--Log output--> 323 <!--Log output-->
324 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file"> 324 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
325 <filter>log_out</filter> 325 <filter>log_out</filter>
497 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 497 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
498 <param name="mode_selector" value="standard" /> 498 <param name="mode_selector" value="standard" />
499 <param name="filter_bits" value="0" /> 499 <param name="filter_bits" value="0" />
500 <conditional name="ont_integration"> 500 <conditional name="ont_integration">
501 <param name="ont_integration_selector" value="set" /> 501 <param name="ont_integration_selector" value="set" />
502 <param name="ul" value="nanopore.first5.fasta.gz" /> 502 <param name="ul" value="nanopore.fasta.gz" />
503 <param name="ul_tip" value="1" /> 503 <param name="ul_tip" value="1" />
504 </conditional> 504 </conditional>
505 <output name="primary_contig_graph" file="hifiasm-out-hifiul.bp.p_ctg.gfa" ftype="gfa1" /> 505 <output name="primary_contig_graph" file="hifiasm-out11-primary.gfa" ftype="gfa1" />
506 <output name="raw_unitigs" file="hifiasm-out-hifiul.bp.r_utg.gfa" ftype="gfa1" /> 506 <output name="raw_unitigs" file="hifiasm-out11-raw.gfa" ftype="gfa1" />
507 </test>
508 <!-- TEST 13: test multi-file nanopore input -->
509 <test expect_num_outputs="6">
510 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
511 <param name="mode_selector" value="standard" />
512 <param name="filter_bits" value="0" />
513 <param name="log_out" value="yes" />
514 <conditional name="ont_integration">
515 <param name="ont_integration_selector" value="set" />
516 <param name="ul" value="nanopore.fasta.gz,nanopore.fasta.gz" />
517 <param name="ul_tip" value="1" />
518 </conditional>
519 <output name="log_file" ftype="txt">
520 <assert_contents>
521 <has_text text="--ul ./ultralong/input_0.fasta.gz,./ultralong/input_1.fasta.gz"/>
522 </assert_contents>
523 </output>
507 </test> 524 </test>
508 </tests> 525 </tests>
509 <help><![CDATA[ 526 <help><![CDATA[
510 .. class:: infomark 527 .. class:: infomark
511 528