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comparison fasterq_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
12 @COPY_CONFIGFILE@ 12 @COPY_CONFIGFILE@
13 @CONFIGURE_RETRY@ 13 @CONFIGURE_RETRY@
14 @SET_ACCESSIONS@ 14 @SET_ACCESSIONS@
15 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do 15 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
16 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} 16 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
17 --seq-defline '@\$sn/\$ri' 17 --seq-defline '$adv.seq_defline'
18 --qual-defline '+' 18 --qual-defline '+'
19 $adv.split 19 $adv.split
20 #if str( $adv.minlen ) != "": 20 #if str( $adv.minlen ) != "":
21 --min-read-len "$adv.minlen" 21 --min-read-len "$adv.minlen"
22 #end if 22 #end if
69 </command> 69 </command>
70 <expand macro="configfile_hack"/> 70 <expand macro="configfile_hack"/>
71 <inputs> 71 <inputs>
72 <expand macro="input_conditional"/> 72 <expand macro="input_conditional"/>
73 <section name="adv" title="Advanced Options" expanded="False"> 73 <section name="adv" title="Advanced Options" expanded="False">
74 <expand macro="defline" defline_param="--seq-defline" defline_default="@$sn/$ri"/>
74 <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="--min-read-len"/> 75 <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="--min-read-len"/>
75 <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end)."> 76 <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end).">
76 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option> 77 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
77 <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option> 78 <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option>
78 <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option> 79 <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option>