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comparison shovill.xml @ 2:f698c7604b3b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 686710a7d313b828f1daed20c4055479727f2d91
author iuc
date Wed, 17 Oct 2018 11:43:35 -0400
parents 57d5928f456e
children 865119fcb694
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1:57d5928f456e 2:f698c7604b3b
15 #else if str($library.lib_type) == "collection" 15 #else if str($library.lib_type) == "collection"
16 --R1 '$library.input1.forward' 16 --R1 '$library.input1.forward'
17 --R2 '$library.input1.reverse' 17 --R2 '$library.input1.reverse'
18 #end if 18 #end if
19 $trim 19 $trim
20 --namefmt "$adv.namefmt" 20 --namefmt '$adv.namefmt'
21 --depth '$adv.depth' 21 --depth '$adv.depth'
22 #if $adv.gsize 22 #if $adv.gsize
23 --gsize '$adv.gsize' 23 --gsize '$adv.gsize'
24 #end if 24 #end if
25 #if $adv.kmers 25 #if $adv.kmers
51 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" /> 51 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />
52 <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" /> 52 <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" />
53 <section name="adv" title="Advanced options" expanded="False"> 53 <section name="adv" title="Advanced options" expanded="False">
54 <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" > 54 <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" >
55 <sanitizer> 55 <sanitizer>
56 <valid initial="string.printable" /> 56 <valid initial="string.printable">
57 <remove value="&apos;" />
58 </valid>
59 <mapping initial="none">
60 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
61 </mapping>
57 </sanitizer> 62 </sanitizer>
58 </param> 63 </param>
59 <param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" /> 64 <param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />
60 <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" /> 65 <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" />
61 <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" /> 66 <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" />