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date Fri, 07 Apr 2017 15:05:57 -0400
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1 <tool id="kaptive" name="Kaptive" version="0.3.0">
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2 <description>reports information about capsular (K) loci found in genome assemblies.</description>
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3 <requirements>
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4 <requirement type="package" version="0.3">kaptive</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
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8 </stdio>
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9 <command><![CDATA[
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10
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11 ln -s "$assembly" "$assembly.name" &&
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12
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13 kaptive.py --assembly "$assembly.name"
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16 --k_refs "$references"
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17 -o 'result'
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18
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19 -t "\${GALAXY_SLOTS:-4}"
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20
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21 #if $allelic_typing:
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22 --allelic_typing "$allelic_typing"
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23 #end if
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24
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25
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26 #if $start_end_margin:
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27 --start_end_margin "$start_end_margin"
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28 #end if
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29
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30 #if $min_gene_cov:
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31 --min_gene_cov "$min_gene_cov"
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32 #end if
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33
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34 #if $min_gene_id:
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35 --min_gene_id "$min_gene_id"
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36 #end if
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37
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38 #if $low_gene_id:
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39 --low_gene_id "$low_gene_id"
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40 #end if
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41
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42 #if $gap_fill_size:
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43 --gap_fill_size "$gap_fill_size"
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44 #end if
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45
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46 ]]></command>
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47 <inputs>
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48
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49 <param name="assembly" type="data" format="fasta" label="Assembly fasta file"/>
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50
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51 <param name="references" type="data" format="genbank" label="Genbank referece K loci"/>
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52
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53 <param name="allelic_typing" type="data" format="fasta" label="Allelic Typing genes" help="SRST2-formatted file of allelic typing genes to include in results" optional="True"/>
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54
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55 <param name="start_end_margin" type="integer" label="Start end margin" help="Missing bases at the ends of K locus allowed in a perfect match. (default: 10)" value="10"/>
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56
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57 <param name="min_gene_cov" type="float" label="Minimum % coverage for genes" help="minimum required % coverage for genes (default: 90.0)" value="90.0"/>
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58
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59 <param name="min_gene_id" type="float" label="Minimum % identity for genes" help="minimum required % identity for genes (default: 80.0)" value="80.0"/>
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60
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61 <param name="low_gene_id" type="float" label="Flag gene with % identity below" help="genes with a % identity below this value will be flagged as low identity (default: 95.0) " value="95.0"/>
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62
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63 <param name="gap_fill_size" type="integer" label="Distance to merge assemblies" help="when separate parts of the assembly are found within this distance, they will be merged (default: 100) " value="100"/>
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65
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66
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67 </inputs>
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68
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69 <outputs>
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70 <data format="tabular" name="results" label="Report Results" from_work_dir="result_table.txt"/>
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71 <data format="txt" name="json" label="JSON Results" from_work_dir="result.json"/>
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72 <data format="fasta" name="fasta" label="Fasta Hit Results" from_work_dir="result_*.fasta" />
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="assembly" value="input.fasta" />
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77 <param name="references" value="Klebsiella_k_locus_primary_reference_db.gbk" />
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78 <output name="results" file="result_table.txt" />
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79 <output name="json" file="result.json" />
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80 <output name="fasta" file="result_input.fasta" />
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81 </test>
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82 </tests>
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83 <help>
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84 <![CDATA[
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85
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86 Documentation available @ https://github.com/katholt/Kaptive/blob/master/README.md
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87
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88
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89 **Acknowledgments**
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90 Tool Wrapper Author: Philip Mabon
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91 ]]>
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92 </help>
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93 <citations>
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94 <citation type="doi">10.5281/zenodo.55773</citation>
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95 </citations>
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96 </tool>