annotate fastqc_report.xml @ 14:2efa46ce2c4c draft

upgrade fastqc_report

<tool id="fastqc_report" name="Fastqc report" version="2.0.0">
    <description>
        Implements FastQC analysis and display results in R Markdown html.
    </description>
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.3">r-rmarkdown</requirement>
        <requirement type="package" version="1.8.4">r-plyr</requirement>
        <requirement type="package" version="1.1.0">r-stringr</requirement>
        <requirement type="package" version="0.5.0">r-highcharter</requirement>
        <requirement type="package" version="0.2">r-dt</requirement>
        <requirement type="package" version="1.4.2">r-reshape2</requirement>
        <requirement type="package" version="4.5.6">r-plotly</requirement>
        <requirement type="package" version="0.2.0.1">r-formattable</requirement>
        <requirement type="package" version="0.3.5">r-htmltools</requirement>
        <requirement type="package" version="0.11.5">fastqc</requirement>
    </requirements>
    <stdio>
        <!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
        <regex match="XXX"
               source="stderr"
               level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command>
        <![CDATA[

        Rscript '${__tool_directory__}/fastqc_report_render.R'
            -e $echo
            -r $reads

		    -o $report
		    -d $report.files_path
		    -s $sink_message

		    -p '${__tool_directory__}/fastqc_report.Rmd'
        ]]>
    </command>
    <inputs>
        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads" type="data"
               label="Short reads data from history"/>
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
               label="Display analysis code in report?"/>
    </inputs>
    <outputs>
        <data format="html" name="report" label="fastqc report"/>
        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
    </outputs>
    <citations>
        <citation type="bibtex">
            @misc{bioinformatics2014fastqc,
            title={FastQC},
            author={Bioinformatics, Babraham},
            year={2014}
            }
        </citation>
        <citation type="bibtex">
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},
            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
            journal={R package version 0.9},
            volume={6},
            year={2016}
            }
        </citation>
        <citation type="bibtex">
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        </citation>
        <citation type="bibtex">
            @misc{plotly2017,
            title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
            author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and
            Marianne Corvellec and Pedro Despouy},
            year = {2017},
            note = {R package version 4.6.0},
            url = {https://CRAN.R-project.org/package=plotly},
            }
        </citation>
        <citation type="bibtex">
            @misc{highcharter2017,
            title = {highcharter: A Wrapper for the 'Highcharts' Library},
            author = {Joshua Kunst},
            year = {2017},
            note = {R package version 0.5.0},
            url = {https://CRAN.R-project.org/package=highcharter},
            }
        </citation>
        <citation type="bibtex">
            @misc{formattable2016,
            title = {formattable: Create 'Formattable' Data Structures},
            author = {Kun Ren and Kenton Russell},
            year = {2016},
            note = {R package version 0.2.0.1},
            url = {https://CRAN.R-project.org/package=formattable},
            }
        </citation>
        <citation>
            @article{ewels2016multiqc,
            title={MultiQC: summarize analysis results for multiple tools and samples in a single report},
            author={Ewels, Philip and Magnusson, M{\aa}ns and Lundin, Sverker and K{\"a}ller, Max},
            journal={Bioinformatics},
            volume={32},
            number={19},
            pages={3047--3048},
            year={2016},
            publisher={Oxford University Press}
            }
        </citation>
    </citations>
</tool>