Mercurial > repos > youyuh48 > nanoplot

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

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planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/NanoPlot
author youyuh48
date Wed, 29 Aug 2018 22:51:00 -0400
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52095f4e027b planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/NanoPlot
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1 <tool id="NanoPlot" name="NanoPlot" version="0.1.0">
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2 <description>Plotting scripts for long read sequencing data</description>
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3 <requirements>
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4 <requirement type="package" version="1.13.0">nanoplot</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
52095f4e027b planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/NanoPlot
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8 NanoPlot
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9 $barcoded
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10 --summary "$input"
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11 -o report
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12 -t \${GALAXY_SLOTS:-1}
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13
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14 && mv report/NanoPlot-report.html output.html
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="input" type="data" format="txt" label="Albacore's summary file"/>
52095f4e027b planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/NanoPlot
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19 <param name="barcoded" type="boolean" label="barcoded" truevalue="--barcoded" falsevalue="" help="Use if you want to split the summary file by barcode"/>
52095f4e027b planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/NanoPlot
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20 </inputs>
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21 <outputs>
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22 <data format="html" name="output" from_work_dir="output.html" label="${tool.name} on ${on_string}"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="sequencing_summary.txt"/>
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27 <output name="output" file="NanoPlot-report.html" ftype="html"/>
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28 </test>
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29 </tests>
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30 <help>
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31 <![CDATA[
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32 usage: NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw] [-o OUTDIR] [-p PREFIX] [--maxlength N]
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33 [--minlength N] [--drop_outliers] [--downsample N] [--loglength] [--percentqual] [--alength]
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34 [--minqual N] [--readtype {1D,2D,1D2}] [--barcoded] [-c COLOR]
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35 [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
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36 [--plots [{kde,hex,dot,pauvre} [{kde,hex,dot,pauvre} ...]]] [--listcolors] [--no-N50] [--N50]
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37 [--title TITLE]
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38 (--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)
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39 ]]>
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40 </help>
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41 <citations>
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42 <citation type="doi">10.1093/bioinformatics/bty149</citation>
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43 </citations>
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44 </tool>