Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
changeset 2:58d48d1157ed draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit b212086a85c4d1e62e0d0c0e77b6f3fcabea04ef-dirty
| author | mingchen0919 |
|---|---|
| date | Mon, 16 Oct 2017 16:53:21 -0400 |
| parents | cd86400bbaed |
| children | b70047273f38 |
| files | fastq_dump_pe.Rmd fastq_dump_pe.xml fastq_dump_se.Rmd fastq_dump_se.xml |
| diffstat | 4 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/fastq_dump_pe.Rmd Tue Oct 10 20:48:29 2017 -0400 +++ b/fastq_dump_pe.Rmd Mon Oct 16 16:53:21 2017 -0400 @@ -30,7 +30,7 @@ sra_accessions = sra_accessions[sra_accessions != ''] # loop through SRA accessions to download and extract reads. for(id in sra_accessions) { - if('FORMAT' == 'fasta') { + if('FORMAT' == 'No') { command = paste0('fastq-dump --fasta --split-files ', '-O read_files_directory ', id) } else { command = paste0('fastq-dump --split-files ', '-O read_files_directory ', id)
--- a/fastq_dump_pe.xml Tue Oct 10 20:48:29 2017 -0400 +++ b/fastq_dump_pe.xml Mon Oct 16 16:53:21 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="rmarkdown_fastq_dump_pe" name="fastq-dump-pe" version="1.0.0"> +<tool id="rmarkdown_fastq_dump_pe" name="fastq-dump-pe" version="1.0.1"> <requirements> <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> @@ -35,7 +35,7 @@ <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" + <param type="boolean" name="format" truevalue="Yes" falsevalue="No" 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?"/>
--- a/fastq_dump_se.Rmd Tue Oct 10 20:48:29 2017 -0400 +++ b/fastq_dump_se.Rmd Mon Oct 16 16:53:21 2017 -0400 @@ -30,7 +30,7 @@ sra_accessions = sra_accessions[sra_accessions != ''] # loop through SRA accessions to download and extract reads. for(id in sra_accessions) { - if('FORMAT' == 'fasta') { + if('FORMAT' == 'No') { command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id) } else { command = paste0('fastq-dump ', '-O read_files_directory ', id)
--- a/fastq_dump_se.xml Tue Oct 10 20:48:29 2017 -0400 +++ b/fastq_dump_se.xml Mon Oct 16 16:53:21 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="rmarkdown_fastq_dump_se" name="fastq-dump-se" version="1.0.0"> +<tool id="rmarkdown_fastq_dump_se" name="fastq-dump-se" version="1.0.1"> <requirements> <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> @@ -35,7 +35,7 @@ <inputs> <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" 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="format" truevalue="Yes" falsevalue="No" 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>