view NanoPlot.xml @ 0:52095f4e027b draft default tip

planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/NanoPlot

<tool id="NanoPlot" name="NanoPlot" version="0.1.0">
  <description>Plotting scripts for long read sequencing data</description>
  <requirements>
    <requirement type="package" version="1.13.0">nanoplot</requirement>
  </requirements>
  <command detect_errors="exit_code">
    <![CDATA[
        NanoPlot
          $barcoded
          --summary "$input"
          -o report
          -t \${GALAXY_SLOTS:-1}

        && mv report/NanoPlot-report.html output.html
    ]]>
  </command>
  <inputs>
    <param name="input" type="data" format="txt" label="Albacore's summary file"/>
    <param name="barcoded" type="boolean" label="barcoded" truevalue="--barcoded" falsevalue="" help="Use if you want to split the summary file by barcode"/>
  </inputs>
  <outputs>
    <data format="html" name="output" from_work_dir="output.html" label="${tool.name} on ${on_string}"/>
  </outputs>
  <tests>
      <test>
          <param name="input" value="sequencing_summary.txt"/>
          <output name="output" file="NanoPlot-report.html" ftype="html"/>
      </test>
  </tests>
  <help>
    <![CDATA[
        usage: NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw] [-o OUTDIR] [-p PREFIX] [--maxlength N]
                [--minlength N] [--drop_outliers] [--downsample N] [--loglength] [--percentqual] [--alength]
                [--minqual N] [--readtype {1D,2D,1D2}] [--barcoded] [-c COLOR]
                [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
                [--plots [{kde,hex,dot,pauvre} [{kde,hex,dot,pauvre} ...]]] [--listcolors] [--no-N50] [--N50]
                [--title TITLE]
                (--fastq file [file ...] | --fasta file [file ...] | --fastq_rich file [file ...] | --fastq_minimal file [file ...] | --summary file [file ...] | --bam file [file ...] | --cram file [file ...] | --pickle pickle)
    ]]>
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/bty149</citation>
  </citations>
</tool>