comparison raven.xml @ 2:3edba9afc9bc draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit a64e791889cae72cf8cf029de8c65fa35d91b16d"

1:f8564b2d7f63

    #set input = "input.fq"
#elif $input_reads.is_of_type("fastq.gz")
    ln -s '$input_reads' ./input.fq.gz &&
    #set input = "input.fq.gz"
#end if
raven 
$weaken
--polishing-rounds '$polishing_rounds'
--match '$match'
--mismatch '$mismatch'
--gap '$gap'
$graphical_fragment_assembly

'$input'
> '$out_fasta'
    ]]></command>
    <inputs>
        <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/>
        <param argument="--weaken" type="boolean" truevalue="--weaken" falsevalue="" label="use larger (k, w); (for use in assembling highly accurate sequences)" checked="false"/>
        <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/>
        <param argument="--match" type="integer" value="3"/>
        <param argument="--mismatch" type="integer" value="-5"/>
        <param argument="--gap" type="integer" value="-4" max="-1"/>
        <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/>

2:3edba9afc9bc

    #set input = "input.fq"
#elif $input_reads.is_of_type("fastq.gz")
    ln -s '$input_reads' ./input.fq.gz &&
    #set input = "input.fq.gz"
#end if
raven
--kmer-len '$kmer_len'
--window-len '$window_len'
--frequency '$frequency'
--polishing-rounds '$polishing_rounds'
--match '$match'
--mismatch '$mismatch'
--gap '$gap'
$graphical_fragment_assembly

'$input'
> '$out_fasta'
    ]]></command>
    <inputs>
        <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/>
        <param argument="--kmer-len" type="integer" value="15" label="Length of minimizers used to find overlaps"/>
        <param argument="--window-len" type="integer" value="5" label="Length of sliding window from which minimizers are sampled"/>
        <param argument="--frequency" type="float" value="0.001" label="Threshold for ignoring most frequent minimizers"/>
        <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/>
        <param argument="--match" type="integer" value="3"/>
        <param argument="--mismatch" type="integer" value="-5"/>
        <param argument="--gap" type="integer" value="-4" max="-1"/>
        <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/>