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1 <tool id="neptune" name="Neptune: Signature Discovery" version="1.2.5.2">
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2 <description>identifies discriminatory sequences between two groups of sequences</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.2.5">neptune</requirement>
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6 </requirements>
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7
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11
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12 <command>
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13 neptune
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14
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15 --inclusion
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16 #for $i in $inclusion
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17 "$i"
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18 #end for
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19
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20 --exclusion
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21 #for $i in $exclusion
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22 "$i"
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23 #end for
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24
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25 #if $options.select == "advanced"
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26
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27 #if $options.kmer:
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28 --kmer "$options.kmer"
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29 #end if
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30
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31 #if $options.rate:
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32 --rate "$options.rate"
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33 #end if
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34
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35 #if $options.exhits:
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36 --exhits "$options.exhits"
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37 #end if
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38
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39 #if $options.size:
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40 --size "$options.size"
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41 #end if
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42
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43 #end if
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44
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45 --output results
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46
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47 --parallelization \${GALAXY_SLOTS:-8}
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48
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49 --organization 3
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50
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51 </command>
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52
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53 <inputs>
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54 <param name="inclusion" type="data_collection" collection_type="list" label="Inclusion" help="The inclusion targets in FASTA format." format="fasta"/>
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55 <param name="exclusion" type="data_collection" collection_type="list" label="Exclusion" help="The exclusion targets in FASTA format." format="fasta"/>
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56
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57 <conditional name="options">
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58 <param name="select" type="select" label="Options Type">
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59 <option value="basic">Basic</option>
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60 <option value="advanced">Advanced</option>
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61 </param>
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62 <when value="basic">
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63 </when>
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64 <when value="advanced">
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65 <param name="kmer" type="integer" label="k" help="The size of the k-mers. This value is automatically calculated if left blank." optional="true"/>
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66 <param name="size" type="integer" label="Size" help=" The minimum size of all reported candidate signatures. Identified candidate signatures shorter than this value will be discard. The default size is 4k." optional="true"/>
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67 <param name="rate" type="float" label="Rate" help="The probability of a mutation or error at an arbitrary position. The default value is 0.01." optional="true" value="0.01"/>
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68 <param name="exhits" type="integer" label="Maximum Exclusion" help="The maximum allowable number of exclusion targets that may contain a k-mer observed in the reference before terminating the construction of a candidate signature." optional="true" value="1"/>
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69 </when>
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70 </conditional>
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71 </inputs>
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72
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73 <outputs>
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74 <data name="consolidated" from_work_dir="results/consolidated/consolidated.fasta" format="fasta" label="Neptune Signatures: $inclusion.name and $exclusion.name"></data>
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75 <data name="receipt" from_work_dir="results/receipt.txt" format="txt" label="Neptune Parameters: $inclusion.name and $exclusion.name"></data>
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76 </outputs>
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77
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78 <tests>
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79 <test>
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80 <output name="receipt"/>
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81 </test>
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82 </tests>
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83
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84 <help>
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85 Neptune locates genomic signatures using an exact k-mer matching strategy while
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86 accommodating k-mer mismatches. The software identifies sequences that are
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87 sufficiently represented within inclusion targets and sufficiently absent from
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88 exclusion targets. The signature discovery process is accomplished using
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89 probabilistic models instead of heuristic strategies.
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90
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91 The inclusion and exclusion targets must be FASTA files.
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92 </help>
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93
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94 <citations>
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95 <citation type="doi">10.1101/032227</citation>
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96 </citations>
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97
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98 </tool>
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