Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
diff mirdeep2.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.xml Tue Aug 08 13:14:41 2017 -0400 @@ -0,0 +1,181 @@ +<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> \ No newline at end of file