annotate mirdeep2.xml @ 4:543ee6fdadeb draft default tip

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty

<tool id="mirdeep2" name="mirdeep2" version="1.0.0">
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <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>
        miRNA identification
    </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[

        Rscript '${__tool_directory__}/mirdeep2_render.R'

            ## 1. input data
            -e $echo
            -a $collapsed_reads
		    -b $reference_genome
		    -c $reads_mapping

            ## 2. output report and report site directory
		    -o $mirdeep2_site
		    -d $mirdeep2_site.files_path
		    -r $csv_result
		    -t $html_result
		    -u $report_log

		    ## other paramters

		    -f $species_mature_mirna
		    -g $related_species_mature_mirna
		    -h $precursor_sequences
		    -j $min_read_stack_height
		    -k $min_score_cutoff
		    -l $randfold_analysis
		    -m $max_precursor_number
		    -n $species
		    -q $switch

		    ## 3. Rmd templates sitting in the tool directory

                ## other Rmd body template files
		        -p  '${__tool_directory__}/mirdeep2.Rmd'


        ]]>
    </command>
    <inputs>
        <param name="collapsed_reads" type="data" format="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"
               label="Reference genome from history"
               help="Reference genome in fasta format"/>
        <param name="reads_mapping" type="data" format="tabular" multiple="False" optional="False"
               label="reads mappings" help="reads mappings in arf format"/>
        <param name="species_mature_mirna" type="data" format="fasta" multiple="False" optional="True"
               label="miRBase mature miRNA for this species"
               help="mature miRNA in fasta format"/>
        <param name="related_species_mature_mirna" type="data" format="fasta" multiple="False" optional="TRUE"
               label="miRBase mature miRNA from related species"
               help="mature miRNA in fasta format"/>
        <param name="precursor_sequences" type="data" format="fasta" multiple="False" optional="TRUE"
               label="precursor sequences" help="miRBase miRNA precursor sequences in fasta format"/>
        <param name="min_read_stack_height" type="integer" argument="-a" optional="True"
               label="minimum read stack height"
               help="minimum read stack height that triggers analysis. Using this option disables
               automatic estimation of the optimal value."/>
        <param name="min_score_cutoff" type="integer" value="0" argument="-b" label="minimum score cut-off"
               help="minimum score cut-off for predicted novel miRNAs to be displayed in the overview
              table. This score cut-off is by default 0."/>
        <param name="randfold_analysis" type="boolean" truevalue="TRUE" falsevalue="FALSE" argument="-c" checked="False"
               label="randfold analysis" help="disable randfold analysis"/>
        <param name="max_precursor_number" type="integer" value="50000" argument="-g" label="maximum number of precursors"
               help="maximum number of precursors to analyze when automatic excision gearing is used.
              default=50000, if set to -1 all precursors will be analyzed"/>
        <param name="species" type="select" label="Search in species">
            <option value="all">All species</option>
            <option value="tni">tetraodon</option>
            <option value="dps">d.pseudoobscura</option>
            <option value="dya">d.yakuba</option>
            <option value="ame">a.mellifera</option>
            <option value="dmo">d.mojavensis</option>
            <option value="cel">worm</option>
            <option value="aga">a.gambiae</option>
            <option value="cbr">c.briggsae</option>
            <option value="cin">c.intestinalis</option>
            <option value="mmu">mouse</option>
            <option value="xtr">x.tropicalis</option>
            <option value="eca">horse</option>
            <option value="cfa">dog</option>
            <option value="fru">fugu</option>
            <option value="bta">cow</option>
            <option value="der">d.erecta</option>
            <option value="dgr">d.grimshawi</option>
            <option value="gga">chicken</option>
            <option value="spu">s.purpuratus</option>
            <option value="bfl">lancelet</option>
            <option value="ptr">chimp</option>
            <option value="dse">d.sechellia</option>
            <option value="dpe">d.persimilis</option>
            <option value="dvi">d.virilis</option>
            <option value="rno">rat</option>
            <option value="dme">d.melanogaster</option>
            <option value="lca">cat</option>
            <option value="sja">c.japonica</option>
            <option value="dan">d.ananassae</option>
            <option value="hsa">human</option>
            <option value="dsi">d.simulans</option>
        </param>
        <param name="switch" type="boolean" truevalue="TRUE" falsevalue="FALSE"
               label="mature_ref_miRNAs contain miRBase v18 identifiers?"
               help="use this switch if mature_ref_miRNAs contain miRBase v18 identifiers (5p and 3p) instead of previous ids from v17"/>


        <param name="echo" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data format="html" name="mirdeep2_site" label="mirdeep2 miRNA identification" />
        <data name="csv_result" format="csv" label="miRNA in csv format" />
        <data name="html_result" format="html" label="miRNA in html format" from_work_dir="result.html"/>
        <data name="report_log" format="txt" label="report log" from_work_dir="result.csv"/>
    </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">
            @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>
    </citations>
</tool>