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planemo upload commit 53d6cab3674d1c73e97cd21f04a3a6e2409bff96
author nml
date Mon, 10 Apr 2017 14:47:17 -0400
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1 <tool id="kaptive" name="Kaptive" version="0.3.0">
2 <description>reports information about capsular (K) loci found in genome assemblies.</description>
3 <requirements>
4 <requirement type="package" version="0.3">kaptive</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
8 </stdio>
9 <command><![CDATA[
10
11 ln -s "$assembly" "$assembly.name" &&
12
13 kaptive.py --assembly "$assembly.name"
14
15
16 --k_refs "$references"
17 -o 'result'
18
19 -t "\${GALAXY_SLOTS:-4}"
20
21 #if $allelic_typing:
22 --allelic_typing "$allelic_typing"
23 #end if
24
25
26 #if $start_end_margin:
27 --start_end_margin "$start_end_margin"
28 #end if
29
30 #if $min_gene_cov:
31 --min_gene_cov "$min_gene_cov"
32 #end if
33
34 #if $min_gene_id:
35 --min_gene_id "$min_gene_id"
36 #end if
37
38 #if $low_gene_id:
39 --low_gene_id "$low_gene_id"
40 #end if
41
42 #if $gap_fill_size:
43 --gap_fill_size "$gap_fill_size"
44 #end if
45
46 ]]></command>
47 <inputs>
48
49 <param name="assembly" type="data" format="fasta" label="Assembly fasta file"/>
50
51 <param name="references" type="data" format="genbank" label="Genbank referece K loci"/>
52
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"/>
54
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"/>
56
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"/>
58
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"/>
60
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"/>
62
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"/>
64
65
66
67 </inputs>
68
69 <outputs>
70 <data format="tabular" name="results" label="Report Results" from_work_dir="result_table.txt"/>
71 <data format="txt" name="json" label="JSON Results" from_work_dir="result.json"/>
72 <data format="fasta" name="fasta" label="Fasta Hit Results" from_work_dir="result_*.fasta" />
73 </outputs>
74 <tests>
75 <test>
76 <param name="assembly" value="input.fasta" />
77 <param name="references" value="Klebsiella_k_locus_primary_reference_db.gbk" />
78 <output name="results" file="result_table.txt" />
79 <output name="json" file="result.json" />
80 <output name="fasta" file="result_input.fasta" />
81 </test>
82 </tests>
83 <help>
84 <![CDATA[
85
86 Documentation available @ https://github.com/katholt/Kaptive/blob/master/README.md
87
88
89 **Acknowledgments**
90 Tool Wrapper Author: Philip Mabon
91 ]]>
92 </help>
93 <citations>
94 <citation type="doi">10.5281/zenodo.55773</citation>
95 </citations>
96 </tool>