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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 13:14:41 -0400 |
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children | 75e53be98c51 |
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<tool id="mirdeep2" name="mirdeep2" 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> 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[ ## Add tools to PATH export PATH=/opt/R-3.2.5/bin:\$PATH && 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"> @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>