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date Thu, 04 May 2017 15:23:54 -0400
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1 <tool id="neptune" name="Neptune: Signature Discovery" version="1.2.5.1">
2 <description>Neptune identifies genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches.</description>
3
4 <requirements>
5 <requirement type="package" version="1.2.5">neptune</requirement>
6 </requirements>
7
8 <stdio>
9 <exit_code range="1:" />
10 </stdio>
11
12 <command>
13 neptune
14
15 --inclusion
16 #for $i in $inclusion
17 "$i"
18 #end for
19
20 --exclusion
21 #for $i in $exclusion
22 "$i"
23 #end for
24
25 #if $options.select == "advanced"
26
27 #if $options.kmer:
28 --kmer "$options.kmer"
29 #end if
30
31 #if $options.rate:
32 --rate "$options.rate"
33 #end if
34
35 #if $options.exhits:
36 --exhits "$options.exhits"
37 #end if
38
39 #if $options.size:
40 --size "$options.size"
41 #end if
42
43 #end if
44
45 --output results
46
47 --parallelization \${GALAXY_SLOTS:-8}
48
49 --organization 3
50
51 </command>
52
53 <inputs>
54 <param name="inclusion" type="data_collection" collection_type="list" label="Inclusion" help="The inclusion targets in FASTA format." format="fasta"/>
55 <param name="exclusion" type="data_collection" collection_type="list" label="Exclusion" help="The exclusion targets in FASTA format." format="fasta"/>
56
57 <conditional name="options">
58 <param name="select" type="select" label="Options Type">
59 <option value="basic">Basic</option>
60 <option value="advanced">Advanced</option>
61 </param>
62 <when value="basic">
63 </when>
64 <when value="advanced">
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"/>
66 <param name="size" type="integer" label="Size" help="The minimum size of reported signatures. The default size is 4k." optional="true"/>
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"/>
68 <param name="exhits" type="integer" label="Minimum Exclusion" help="The minimum number of inclusion targets that must contain a k-mer observed in the reference to begin or continue building candidate signatures. This will be calculated if not specified." optional="true" value="1"/>
69 </when>
70 </conditional>
71 </inputs>
72
73 <outputs>
74 <data name="consolidated" from_work_dir="results/consolidated/consolidated.fasta" format="fasta" label="Neptune Signatures: $inclusion.name and $exclusion.name"></data>
75 <data name="receipt" from_work_dir="results/receipt.txt" format="txt" label="Neptune Parameters: $inclusion.name and $exclusion.name"></data>
76 </outputs>
77
78 <tests>
79 <test>
80 <output name="receipt"/>
81 </test>
82 </tests>
83
84 <help>
85 Neptune locates genomic signatures using an exact k-mer matching strategy while
86 accommodating k-mer mismatches. The software identifies sequences that are
87 sufficiently represented within inclusion targets and sufficiently absent from
88 exclusion targets. The signature discovery process is accomplished using
89 probabilistic models instead of heuristic strategies.
90
91 The inclusion and exclusion targets must be FASTA files.
92 </help>
93
94 <citations>
95 <citation type="doi">10.1101/032227</citation>
96 </citations>
97
98 </tool>