Mercurial > repos > iuc > miniasm
comparison miniasm.xml @ 3:73a3846701e1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 5b819c9a19a38ebdd60bcd0ea3f530bf60a688bb"
author | iuc |
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date | Fri, 02 Apr 2021 20:20:44 +0000 |
parents | 8dee0218ac7d |
children | a7b889b90140 |
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2:8dee0218ac7d | 3:73a3846701e1 |
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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"/> |