Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
diff 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
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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mirdeep2_mapper.xml Tue Aug 08 13:14:41 2017 -0400 @@ -0,0 +1,135 @@ +<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> \ No newline at end of file