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1 <tool id="skesa" name="skesa" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="2.2">skesa</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 #if $jobtype.select != "cl"
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7 skesa
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8 #if $jobtype.select == "srr"
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9 -sra_run $srrnum
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10 #else if $jobtype.select == "asm"
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11 --fasta $draft
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12 #else if $jobtype.select == "se"
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13 --fastq $fastq1
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14 #else if $jobtype.select == "pe"
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15 --fastq $fastq1,$fastq2 --use_paired_ends
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16 #else if $jobtype.select == "rp"
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17 --fastq $pairedf.forward,$pairedf.reverse --use_paired_ends
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18 #end if
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19 #if $cores != 0
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20 --cores $cores
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21 #end if
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22 --memory $memory > results.skesa.fasta
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23 #end if
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24
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25 ]]></command>
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26 <inputs>
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27 <conditional name="jobtype">
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28 <when value="srr">
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29 <param name="srrnum" type="text" label="Sra run number"/>
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30 </when>
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31 <param name="select" type="select" label="Assembly or FASTQ Reads?">
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32 <option value="sra">SRR number</option>
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33 <option value="asm">Genome Assembly</option>
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34 <option value="se">Single-End Reads</option>
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35 <option value="pe">Paired-End Reads (Separate Files)</option>
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36 <option value="rp">Paired-End Reads (Paired Data Set)</option>
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37 <option value="cl">Collection of Reads</option>
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38 </param>
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39 <when value="asm">
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40 <param name="draft" type="data" format="fasta" label="FASTA" />
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41 </when>
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42 <when value="se">
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43 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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44 </when>
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45 <when value="pe">
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46 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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47 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
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48 </when>
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49 <when value="cl">
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50 <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" />
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51 </when>
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52 <when value="rp">
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53 <param type="data_collection" collection_type="paired" name="pairedf" format="fastq" label="FASTQS: Must be a paired set of forward and reverse fastq files" />
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54 </when>
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55 </conditional>
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56 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
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57 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />
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58 <param name="kmer" type="integer" label="Minimal kmer length for assembly [default 21] if non are specified " value="0" />
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59 <param name="min_count" type="integer" label="Minimal count for kmers retained for comparing alternate choices [integer]" value="0" />
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60
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61 </inputs>
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62 <outputs>
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63 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
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64 </outputs>
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65
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66 <help><![CDATA[
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67
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68 **Usage: skesa**
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69
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70 **INPUT**
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71
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72 A fasta assembly or single or paired end reads test or data set list of fastqs
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73
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74 **Memory available**
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75
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76 --memory arg (=32) Memory available (GB) [integer]
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77
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78
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79 **Number of cores**
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80
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81 --cores arg (=0) Number of cores to use (default all) [integer]
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82
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83 https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/
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84
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85 ]]></help>
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86 <citations>
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87 <citation type="bibtex">
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88 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
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89 title={skesa: eSKESA is a de-novo sequence read assembler for cultured single isolate genomes
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90 based on DeBruijn graphs. It uses conservative heuristics and is designed to
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91 create breaks at repeat regions in the genome. This leads to excellent sequence
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92 quality but not necessarily a large N50 statistic. It is a multi-threaded
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93 application that scales well with the number of processors. For different runs
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94 with the same inputs, including the order of reads, the order and orientation
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95 of contigs in the output is deterministic. },
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96 url={https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/},
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97 author={National Center for Biotechnology Information },
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98 }</citation>
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99 </citations>
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100 </tool>
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