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comparison flye.xml @ 10:cb8dfd28c16f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
author bgruening
date Wed, 26 Oct 2022 13:37:35 +0000
parents 276f5d8712d5
children 291923e6f276
comparison
equal deleted inserted replaced
9:276f5d8712d5 10:cb8dfd28c16f
37 --asm-coverage $asm.asm_coverage 37 --asm-coverage $asm.asm_coverage
38 -g '${asm.genome_size}' 38 -g '${asm.genome_size}'
39 #end if 39 #end if
40 $meta 40 $meta
41 $scaffold 41 $scaffold
42 $no_alt_contigs
42 ]]></command> 43 ]]></command>
43 <inputs> 44 <inputs>
44 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" /> 45 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
45 <conditional name="mode_conditional"> 46 <conditional name="mode_conditional">
46 <param name="mode" type="select" label="Mode"> 47 <param name="mode" type="select" label="Mode">
95 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator> 96 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
96 </param> 97 </param>
97 </when> 98 </when>
98 <when value="false" /> 99 <when value="false" />
99 </conditional> 100 </conditional>
101 <param argument="--no-alt-contigs" type="boolean" truevalue="--no-alt-contigs" falsevalue="" checked="false" label="Remove all non-primary contigs from the assembly"/>
100 <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/> 102 <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/>
101 </inputs> 103 </inputs>
102 <outputs> 104 <outputs>
103 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/> 105 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/>
104 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/> 106 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/>
319 <assert_contents> 321 <assert_contents>
320 <has_size value="427129" delta="100"/> 322 <has_size value="427129" delta="100"/>
321 </assert_contents> 323 </assert_contents>
322 </output> 324 </output>
323 </test> 325 </test>
326 <!--Test 09: test not-alt-contigs parameter w-->
327 <test expect_num_outputs="4">
328 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
329 <param name="mode" value="--nano-raw"/>
330 <param name="iterations" value="0"/>
331 <param name="no_alt_contigs" value="true"/>
332 <output name="assembly_info" ftype="tabular">
333 <assert_contents>
334 <has_size value="151" delta="100"/>
335 </assert_contents>
336 </output>
337 <output name="assembly_graph" ftype="graph_dot">
338 <assert_contents>
339 <has_size value="217" delta="100"/>
340 </assert_contents>
341 </output>
342 <output name="assembly_gfa" ftype="txt">
343 <assert_contents>
344 <has_size value="5110" delta="100"/>
345 </assert_contents>
346 </output>
347 <output name="consensus" ftype="fasta">
348 <assert_contents>
349 <has_size value="5123" delta="100"/>
350 </assert_contents>
351 </output>
352 </test>
324 </tests> 353 </tests>
325 <help><![CDATA[ 354 <help><![CDATA[
326 355
327 .. class:: infomark 356 .. class:: infomark
328 357