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annotate skesa.xml @ 21:8bafd3d18864 draft

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author cstrittmatter
date Mon, 17 Sep 2018 06:49:22 -0400
parents a368d48a4562
children 9448df7c25a0
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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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7 skesa
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8 #if $jobtype.select == "asm"
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9 --fasta $draft
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10 #else if $jobtype.select == "se"
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11 --fastq $fastq
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12 #else if $jobtype.select == "cl"
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13 #set forward=$jobtype.coll.forward
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14 #set reverse=$jobtype.coll.reverse
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15 --fastq $forward,$reverse --use_paired_ends
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16 #else if $jobtype.select == "pe"
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17 --fastq $forward,$reverse --use_paired_ends
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19 #end if
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20 #if $cores != 0
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21 --cores $cores
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22 #end if
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23 --memory $memory > results.skesa.fasta
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26 ]]></command>
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27 <inputs>
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28 <conditional name="jobtype">
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29 <param name="select" type="select" label="Assembly or FASTQ Reads?">
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30 <option value="asm">Genome Assembly</option>
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31 <option value="se">Single-End Reads</option>
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32 <option value="pe">Paired-End Reads (Separate Files)</option>
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33 <option value="cl">Paired collection from your history</option>
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34 </param>
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35 <when value="asm">
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36 <param name="draft" type="data" format="fasta" label="FASTA" />
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37 </when>
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38 <when value="se">
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39 <param name="fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
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40 </when>
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41 <when value="cl">
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42 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
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43 </when>
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44 <when value="pe">
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45 <param name="forward" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
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46 <param name="reverse" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
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47 </when>
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48 </conditional>
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49 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
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50 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />
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51
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52 </inputs>
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53 <outputs>
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54 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
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55 </outputs>
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57 <help><![CDATA[
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58
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59 **Usage: skesa**
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61 **INPUT**
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63 A fasta assembly or single or paired end reads test or data set list of fastqs
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65 **Memory available**
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67 --memory arg (=32) Memory available (GB) [integer]
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70 **Number of cores**
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72 --cores arg (=0) Number of cores to use (default all) [integer]
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73
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74 https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/
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75
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76 ]]></help>
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77 <citations>
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78 <citation type="bibtex">
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79 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
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80 title={skesa: eSKESA is a de-novo sequence read assembler for cultured single isolate genomes
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81 based on DeBruijn graphs. It uses conservative heuristics and is designed to
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82 create breaks at repeat regions in the genome. This leads to excellent sequence
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83 quality but not necessarily a large N50 statistic. It is a multi-threaded
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84 application that scales well with the number of processors. For different runs
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85 with the same inputs, including the order of reads, the order and orientation
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86 of contigs in the output is deterministic. },
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87 url={https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/},
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88 author={National Center for Biotechnology Information },
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89 }</citation>
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90 </citations>
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91 </tool>