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comparison miniasm.xml @ 3:73a3846701e1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 5b819c9a19a38ebdd60bcd0ea3f530bf60a688bb"
author iuc
date Fri, 02 Apr 2021 20:20:44 +0000
parents 8dee0218ac7d
children a7b889b90140
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2:8dee0218ac7d 3:73a3846701e1
1 <tool id="miniasm" name="miniasm" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="miniasm" name="miniasm" version="@TOOL_VERSION@+galaxy1">
2 <description>Ultrafast de novo assembly for long noisy reads </description> 2 <description>Ultrafast de novo assembly for long noisy reads </description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.3</token> 4 <token name="@TOOL_VERSION@">0.3</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
23 -n '$graph.nRounds' 23 -n '$graph.nRounds'
24 -F '$graph.finalDropRatio' 24 -F '$graph.finalDropRatio'
25 '$paf' > '$gfa' 25 '$paf' > '$gfa'
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <param name="readFile" type="data" format="fastq,fasta" label="Sequence Reads" /> 28 <param name="readFile" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Sequence Reads" />
29 <param name="paf" type="data" format="tabular" label="PAF file" help="Pairwise mapping format" /> 29 <param name="paf" type="data" format="tabular" label="PAF file" help="Pairwise mapping format" />
30 <section name="preselection" title="Preselection options"> 30 <section name="preselection" title="Preselection options">
31 <param argument="-m" name="minMatch" type="integer" value="100" label="Drop mappings having less than this number of matching bases" 31 <param argument="-m" name="minMatch" type="integer" value="100" label="Drop mappings having less than this number of matching bases"
32 help="column 10 in PAF"/> 32 help="column 10 in PAF"/>
33 <param argument="-i" name="minIden" type="float" value="0.05" label="During read filtering, ignore mappings with col10/col11 below this value" 33 <param argument="-i" name="minIden" type="float" value="0.05" label="During read filtering, ignore mappings with col10/col11 below this value"
63 <param name="readFile" value="mini_reads.fq"/> 63 <param name="readFile" value="mini_reads.fq"/>
64 <param name="paf" value="mini_reads.paf.gz"/> 64 <param name="paf" value="mini_reads.paf.gz"/>
65 <output name="gfa" file="mini_reads.gfa"/> 65 <output name="gfa" file="mini_reads.gfa"/>
66 </test> 66 </test>
67 <test> 67 <test>
68 <param name="readFile" value="mini_reads.fq"/> 68 <param name="readFile" value="mini_reads.fq.gz"/>
69 <param name="minMatch" value="99"/> 69 <param name="minMatch" value="99"/>
70 <param name="minIden" value="0.04"/> 70 <param name="minIden" value="0.04"/>
71 <param name="minSpan" value="999"/> 71 <param name="minSpan" value="999"/>
72 <param name="minCov" value="2"/> 72 <param name="minCov" value="2"/>
73 <param name="minOvlp" value="999"/> 73 <param name="minOvlp" value="999"/>