view abayesqr.xml @ 0:598c3e720567 draft default tip

planemo upload commit 4a2876135fca2f46ffa6451e463eb167a0b51b65

<?xml version="1.0"?>
<tool id="abayesqr" name="aBayesQR" version="1.0.0">
    <description>for haplotype reconstruction</description>
    <requirements>
        <requirement type="package" version="1.0.0">abayesqr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$reference' input.fasta &&
        ln -s '$input' input.sam &&
        aBayesQR $abayes_params &&
        python '$__tool_directory__/parse_output.py'
        ]]>
    </command>
    <configfiles>
        <configfile name="abayes_params"><![CDATA[filename of reference sequence (FASTA) : input.fasta
filname of the aligned reads (sam format) : input.sam
paired-end (1 = true, 0 = false) : $paired
SNV_thres : $snv
reconstruction_start : $start
reconstruction_stop: $stop
min_mapping_qual : $qual
min_read_length : $readlength
max_insert_length : $insertlength
characteristic zone name : test
seq_err (assumed sequencing error rate(%)) : $seq_err
MEC improvement threshold : $mec_threshold
]]></configfile>
    </configfiles>
    <inputs>
        <param name="input" type="data" format="sam" label="Input reads in SAM format" />
        <param name="reference" type="data" format="fasta" label="Reference genome" />
        <param name="paired" type="boolean" truevalue="1" falsevalue="0" label="Paired reads" />
        <param name="snv" type="float" value="0.01" label="SNV threshold" />
        <param name="start" type="integer" value="1" label="Reconstruction start" />
        <param name="stop" type="integer" value="1300" label="Reconstruction stop" />
        <param name="qual" type="integer" value="60" label="Minimum mapping quality" />
        <param name="readlength" type="integer" value="150" label="Minimum read length" />
        <param name="insertlength" type="integer" value="250" label="Maximum insert length" />
        <param name="seq_err" type="float" value="0.1" label="Sequencing error rate" />
        <param name="mec_threshold" type="float" value="0.0395" label="MEC improvement threshold" />
    </inputs>
    <outputs>
        <data name="haplotypes" from_work_dir="haplotypes.fasta" format="fasta" label="${tool.name} on ${on_string} - Haplotypes" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="sam" value="test-data/simulated.sam" />
            <param name="reference" ftype="fasta" value="test-data/pol.fasta" />
            <output name="haplotypes" file="test-data/haplotypes.fasta" />
        </test>
    </tests>
    <help>
    </help>
    <citations>
        <citation type="doi">10.1089/cmb.2017.0249</citation>
    </citations>
</tool>