Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
view fastq_dump_pe.xml @ 1:cd86400bbaed draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit ea6df97960569d247d64be1549aa90768c9786f4
author | mingchen0919 |
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date | Tue, 10 Oct 2017 20:48:29 -0400 |
parents | 1a11c4fd13d0 |
children | 58d48d1157ed |
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<tool id="rmarkdown_fastq_dump_pe" name="fastq-dump-pe" version="1.0.0"> <requirements> <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> <requirement type="package" version="1.2">r-rmarkdown</requirement> <requirement type="package" version="0.3.5">r-htmltools</requirement> <requirement type="package" version="0.5.0">r-dplyr</requirement> <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement> </requirements> <description> Download and extract paired end reads in fastq or fasta format from NCBI SRA. The output is a list of paired datasets collection. </description> <stdio> <!--All stderr are redirected to a file. "XXX" is used to match with nothing--> <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/> </stdio> <command> <![CDATA[ Rscript '${__tool_directory__}/fastq_dump_pe_render.R' -i '$sra_accession' -e $echo -f $format -r $report -d $report.files_path -s $sink_message -t '${__tool_directory__}/fastq_dump_pe.Rmd' ]]> </command> <inputs> <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false" help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/> <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true" label="output files in fastq (Yes) or fasta (No)?"/> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?"/> </inputs> <outputs> <data format="html" name="report" label="Fastq-dump report" /> <collection type="list:paired" name="list_collection" label="Fastq-dump (paired end reads)"> <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" directory="read_files_directory"/> </collection> <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" /> </outputs> </tool>