Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
diff fastq_dump_pe.xml @ 0:1a11c4fd13d0 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
author | mingchen0919 |
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date | Wed, 27 Sep 2017 21:41:29 -0400 |
parents | |
children | cd86400bbaed |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_dump_pe.xml Wed Sep 27 21:41:29 2017 -0400 @@ -0,0 +1,50 @@ +<tool id="rmarkdown_fastqc_dump_pe" name="fastqc-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> \ No newline at end of file