Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
view mirdeep2_mapper.xml @ 3:228117ad62bb draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 14:34:03 -0400 |
parents | 90207652b06a |
children | 543ee6fdadeb |
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<tool id="mirdeep2_mapper_site" name="mirdeep2_mapper" version="1.0.0"> <requirements> <requirement type="package" version="1.19.2.1">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> 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[ 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"> @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>