annotate mirdeep2_mapper.xml @ 0:963905bcb754 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty

<tool id="mirdeep2_mapper_site" name="mirdeep2_mapper" version="1.0.0">
    <requirements>
        <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.2">r-rmarkdown</requirement>
        <requirement type="package" version="1.8.4">r-plyr</requirement>
        <requirement type="package" version="0.5.0">r-dplyr</requirement>
        <requirement type="package" version="0.3.5">r-htmltools</requirement>
    </requirements>
    <description>
        Mapping reads to genome
    </description>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"
               description="Execution halted." />
        <regex match="Error in"
               source="both"
               level="fatal"
               description="An undefined error occured, please check your intput carefully and contact your administrator." />
        <regex match="Fatal error"
               source="both"
               level="fatal"
               description="An undefined error occured, please check your intput carefully and contact your administrator." />
    </stdio>
    <command>
        <![CDATA[
        ## Add tools to PATH
        export PATH=/opt/R-3.2.5/bin:\$PATH &&

        Rscript '${__tool_directory__}/mirdeep2_mapper_render.R'

            ## 1. input data
            -r $reads
            -g $reference_genome
            -e $echo

            ## 2. output report and report site directory
		    -o $mirdeep2_mapper_site
		    -d $mirdeep2_mapper_site.files_path
		    -m $reads_collapsed
		    -n $reads_collapsed_vs_genome
		    -t $report_log

		    ## other parameters
		    -b $parse_to_fasta
		    -c $clean_entries
		    -f $clip_3_adapter
		    -h $discard_shorter_reads
		    -j $collapse_reads_or_not
		    -k $map_with_one_mismatch
		    -l $map_up_to_position


		    ## 3. Rmd templates sitting in the tool directory

                ## other Rmd body template files
		        -p '${__tool_directory__}/mirdeep2_mapper.Rmd'



        ]]>
    </command>
    <inputs>
        <param name="reads" type="data" format="fastq,fasta" multiple="False" optional="False"
               label="Read input file" help="Reads in fastq or fasta format"/>
        <param name="reference_genome" type="data" format="fasta" multiple="false" optional="False" argument="-p"
               label="Reference genome from history" />

        <param name="parse_to_fasta" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-h"
               optional="True" label="Parse to fasta format" />
        <param name="clean_entries" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-j"
               optional="True" label="Remove reads with non-canonical letters"
               help="remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N" />
        <param name="clip_3_adapter" type="text" argument="-k" value="" optional="true" label="Clip 3' adapter sequence (optional)"
               help="Enter an adapter sequence"/>
        <param name="discard_shorter_reads" type="integer" min="0" value="18" argument="-l"
               label="Discard reads shorter than int nts" />
        <param name="collapse_reads_or_not" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-m"
               label="Collapse reads" />
        <param name="map_with_one_mismatch" type="boolean" truevalue="TRUE" falsevalue="FALSE" argument="-q"
               label="Map with one mismatch"
               help="map with one mismatch in the seed (mapping takes longer)"/>
        <param name="map_up_to_position" type="integer" min="1" value="5" label="Map up to int nts" argument="-r"
               help="A read is allowed to map up to this number of positions in the genome. Default is 5"/>

        <param name="echo" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data name="mirdeep2_mapper_site" format="html" label="mirdeep2_mapper site" />
        <data name="reads_collapsed" format="fasta" label="reads_collapsed" />
        <data name="reads_collapsed_vs_genome" format="tabular" label="reads_collapsed_vs_ref_genome" />
        <data name="report_log" format="txt" label="report log"/>
    </outputs>
    <citations>
        @article{friedlander2011mirdeep2,
        title={miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades},
        author={Friedl{\"a}nder, Marc R and Mackowiak, Sebastian D and Li, Na and Chen, Wei and Rajewsky, Nikolaus},
        journal={Nucleic acids research},
        volume={40},
        number={1},
        pages={37--52},
        year={2011},
        publisher={Oxford University Press}
        }
        <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">
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        </citation>
    </citations>
</tool>