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comparison fastq_dump.xml @ 30:4317d3cb6cba draft

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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
comparison
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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"/>