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comparison hifiasm.xml @ 15:60024a528cbd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4
author bgruening
date Fri, 13 Oct 2023 07:26:01 +0000
parents 71740308d412
children 41cea2aa2dce
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14:71740308d412 15:60024a528cbd
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@">0.19.5</token> 4 <token name="@TOOL_VERSION@">0.19.7</token>
5 <token name="@VERSION_SUFFIX@">0</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>
111 #if $purge_options.purge_max: 111 #if $purge_options.purge_max:
112 --purge-max $purge_options.purge_max 112 --purge-max $purge_options.purge_max
113 #end if 113 #end if
114 #if $purge_options.n_hap: 114 #if $purge_options.n_hap:
115 --n-hap $purge_options.n_hap 115 --n-hap $purge_options.n_hap
116 #end if
117 #end if
118 #if str($scaffolding_options.scaffold_selector) == 'set':
119 --dual-scaf
120 #if $scaffolding_options.scaf_gap:
121 --scaf-gap $scaffolding_options.scaf_gap
116 #end if 122 #end if
117 #end if 123 #end if
118 124
119 #if str($hic_partition.hic_partition_selector) == 'set': 125 #if str($hic_partition.hic_partition_selector) == 'set':
120 --h1 ${ ','.join(["'%s'" % $x for $x in $hic1_inputs]) } 126 --h1 ${ ','.join(["'%s'" % $x for $x in $hic1_inputs]) }
271 </sanitizer> 277 </sanitizer>
272 <validator type="regex">[0-9kKmMGg]+</validator> 278 <validator type="regex">[0-9kKmMGg]+</validator>
273 </param> 279 </param>
274 </when> 280 </when>
275 </conditional> 281 </conditional>
282 <conditional name="scaffolding_options">
283 <param name="scaffold_selector" type="select" label="Options for hifiasm scaffolding">
284 <option value="blank">No scaffolding (default)</option>
285 <option value="set">Turn on hifiasm scaffolding</option>
286 </param>
287 <when value="blank" />
288 <when value="set">
289 <param argument="--scaf-gap" type="integer" min="1" value="3000000" optional="true" label="Max scaffolding gap size" help="Set the max gap size of scaffolds (default is 3,000,000)" />
290 </when>
291 </conditional>
276 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no" /> 292 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no" />
277 <param name="bins_out" type="boolean" label="Output .bin files (used for development and debugging)?" truevalue="yes" falsevalue="no" /> 293 <param name="bins_out" type="boolean" label="Output .bin files (used for development and debugging)?" truevalue="yes" falsevalue="no" />
278 </inputs> 294 </inputs>
279 <outputs> 295 <outputs>
280 <!--Standard mode--> 296 <!--Standard mode-->