Mercurial > repos > petr-novak > re_utils
changeset 15:a675b4534b19 draft
Uploaded
| author | petr-novak |
|---|---|
| date | Fri, 24 Apr 2020 08:53:51 -0400 |
| parents | 62fefa284036 |
| children | 5376e1c9adec |
| files | sampleFasta.xml |
| diffstat | 1 files changed, 9 insertions(+), 8 deletions(-) [+] |
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--- a/sampleFasta.xml Fri Feb 07 06:06:47 2020 -0500 +++ b/sampleFasta.xml Fri Apr 24 08:53:51 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="sampler" name="Read sampling" version="1.0.0"> +<tool id="sampler" name="Read sampling" version="1.0.1"> <description> Tool for random sampling subsets of reads from larger dataset</description> <requirements> <requirement type="package">seqkit</requirement> @@ -11,24 +11,25 @@ #if str($paired)=="true" ${__tool_directory__}/deinterlacer.py $input Afile Bfile && - seqkit sample -2 --number $number --rand-seed $seed -o Asample -w 0 Afile < /dev/null + NUMBER=\$(($(number) / 2)) && - seqkit sample -2 --number $number --rand-seed $seed -o Bsample -w 0 Bfile < /dev/null + seqkit sample -2 --number \$NUMBER --rand-seed $seed -o Asample -w 0 Afile < /dev/null + && + seqkit sample -2 --number \$NUMBER --rand-seed $seed -o Bsample -w 0 Bfile < /dev/null && ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile #else - seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input + seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input < /dev/null #end if ]]> </command> <inputs> <param format="fasta" type="data" name="input" label="Read file (FASTA)" /> - <param name="number" type="integer" size="7" value="500000" min="1" label="Number of reads or read pairs"/> + <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Paired-end reads" help="If paired-end reads are sampled, left and right-hand reads must be interlaced and all pairs must be complete."/> + <param name="number" type="integer" size="7" value="500000" min="1" label="Number of reads"/> <param name="seed" type="integer" size="10" value="10" min="0" label="Random number generator seed " /> - <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Paired-end reads" help="If paired-end reads are sampled, left and right-hand reads must be interlaced and all pairs must be complete."/> - - + </inputs>