Mercurial > repos > iuc > sra_tools
comparison fastq_dump.xml @ 30:4317d3cb6cba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
| author | iuc |
|---|---|
| date | Mon, 11 Sep 2023 08:37:23 +0000 |
| parents | 9a776b080193 |
| children | 734abc7ac21d |
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| 29:6ea73833cf67 | 30:4317d3cb6cba |
|---|---|
| 20 prefetch -X 200000000 "\$acc" && | 20 prefetch -X 200000000 "\$acc" && |
| 21 #end if | 21 #end if |
| 22 fastq-dump --accession "\$acc" | 22 fastq-dump --accession "\$acc" |
| 23 --split-files | 23 --split-files |
| 24 #end if | 24 #end if |
| 25 --defline-seq '@\$sn[_\$rn]/\$ri' | 25 --defline-seq '$adv.defline_seq' |
| 26 --defline-qual '+' | 26 --defline-qual '+' |
| 27 | 27 |
| 28 $adv.split | 28 $adv.split |
| 29 #if str( $adv.alignments ) == "aligned": | 29 #if str( $adv.alignments ) == "aligned": |
| 30 --aligned | 30 --aligned |
| 89 <option value="fastqsanger.gz">gzip compressed fastq</option> | 89 <option value="fastqsanger.gz">gzip compressed fastq</option> |
| 90 <option value="fastqsanger">Uncompressed fastq</option> | 90 <option value="fastqsanger">Uncompressed fastq</option> |
| 91 <option value="fastqsanger.bz2">bzip2 compressed fastq</option> | 91 <option value="fastqsanger.bz2">bzip2 compressed fastq</option> |
| 92 </param> | 92 </param> |
| 93 <section name="adv" title="Advanced Options" expanded="False"> | 93 <section name="adv" title="Advanced Options" expanded="False"> |
| 94 <expand macro="defline" defline_param="--defline-seq" defline_default="@$sn[_$rn]/$ri"/> | |
| 94 <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/> | 95 <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/> |
| 95 <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/> | 96 <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/> |
| 96 <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/> | 97 <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/> |
| 97 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="" label="Split spot by read pairs" help="Split spots into individual reads." argument="--split-spot"/> | 98 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="" label="Split spot by read pairs" help="Split spots into individual reads." argument="--split-spot"/> |
| 98 <expand macro="alignments"/> | 99 <expand macro="alignments"/> |