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comparison skesa.xml @ 5:b82a1b3c5b61 draft

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planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
author cstrittmatter
date Wed, 15 Aug 2018 17:35:46 -0400
parents 15be58c254f5
children f9b8095f18fe
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4:15be58c254f5 5:b82a1b3c5b61
3 <requirement type="package" version="2.2">skesa</requirement> 3 <requirement type="package" version="2.2">skesa</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 #if $jobtype.select != "cl" 6 #if $jobtype.select != "cl"
7 skesa 7 skesa
8 #if $jobtype.select == "asm" 8 #if $jobtype.select == "srr"
9 -i $draft 9 -sra_run $srrnum
10 #else if $jobtype.select == "asm"
11 --fasta $draft
10 #else if $jobtype.select == "se" 12 #else if $jobtype.select == "se"
11 --fastq $fastq1 13 --fastq $fastq1
12 #else if $jobtype.select == "pe" 14 #else if $jobtype.select == "pe"
13 --fastq $fastq1,$fastq2 --use_paired_ends 15 --fastq $fastq1,$fastq2 --use_paired_ends
14 #end if 16 #end if
15 > results.skesa.fasta 17 #if $cores != 0
18 --cores $cores
19 #end if
20 --memory $memory > results.skesa.fasta
16 #end if 21 #end if
17 22
18 ]]></command> 23 ]]></command>
19 <inputs> 24 <inputs>
20 <conditional name="jobtype"> 25 <conditional name="jobtype">
26 <when value="srr">
27 <param name="srrnum" type="text" label="Sra run number"/>
28 </when>
21 <param name="select" type="select" label="Assembly or FASTQ Reads?"> 29 <param name="select" type="select" label="Assembly or FASTQ Reads?">
30 <option value="sra">SRR number</option>
22 <option value="asm">Genome Assembly</option> 31 <option value="asm">Genome Assembly</option>
23 <option value="se">Single-End Reads</option> 32 <option value="se">Single-End Reads</option>
24 <option value="pe">Paired-End Reads</option> 33 <option value="pe">Paired-End Reads</option>
25 <option value="cl">Collection of Reads</option> 34 <option value="cl">Collection of Reads</option>
26 </param> 35 </param>
36 </when> 45 </when>
37 <when value="cl"> 46 <when value="cl">
38 <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" /> 47 <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
39 </when> 48 </when>
40 </conditional> 49 </conditional>
41 50 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
42 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" /> 51 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />
43 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" /> 52 <param name="kmer" type="integer" label="Minimal kmer length for assembly [default 21] if non are specified " value="0" />
53 <param name="min_count" type="integer" label="Minimal count for kmers retained for comparing alternate choices [integer]" value="0" />
44 54
45 </inputs> 55 </inputs>
46 <outputs> 56 <outputs>
47 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/> 57 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
48 </outputs> 58 </outputs>
53 63
54 **INPUT** 64 **INPUT**
55 65
56 A fasta assembly or single or paired end reads test or data set list of fastqs 66 A fasta assembly or single or paired end reads test or data set list of fastqs
57 67
58 **PERCENTIDENTITY** 68 **Memory available**
59 69
60 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. 70 --memory arg (=32) Memory available (GB) [integer]
71
61 72
62 **PERCENTLENGTH** 73 **Number of cores**
63 74
64 Percentage of length wanted to use against the database. From 0 to 100, default is 50%. 75 --cores arg (=0) Number of cores to use (default all) [integer]
65 76
66 https://github.com/phac-nml/ecoli_serotyping 77 https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/
67 78
68 ]]></help> 79 ]]></help>
69 <citations> 80 <citations>
70 <citation type="bibtex"> 81 <citation type="bibtex">
71 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014, 82 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
72 title={SRST2: ecyper wraps a standalone serotyping module for Escherichia coli. Supports fasta and fastq file formats.}, 83 title={skesa: eSKESA is a de-novo sequence read assembler for cultured single isolate genomes
73 url={https://www.nml-lnm.gc.ca/}, 84 based on DeBruijn graphs. It uses conservative heuristics and is designed to
74 author={National Microbiology Laboratory }, 85 create breaks at repeat regions in the genome. This leads to excellent sequence
86 quality but not necessarily a large N50 statistic. It is a multi-threaded
87 application that scales well with the number of processors. For different runs
88 with the same inputs, including the order of reads, the order and orientation
89 of contigs in the output is deterministic. },
90 url={https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/},
91 author={National Center for Biotechnology Information },
75 }</citation> 92 }</citation>
76 </citations> 93 </citations>
77 </tool> 94 </tool>