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"planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
author nml
date Thu, 21 Nov 2019 12:53:20 -0500
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1 <tool id="abacas" name="abacas contig ordering" version="1.1">
2 <description>Order and Orientate Contigs </description>
3 <requirements>
4 <requirement type="package" version="3.23">mummer</requirement>
5 <requirement type="package" version="5.26.2">perl</requirement>
6 </requirements>
7 <command detect_errors="exit_code">
8 bash '$__tool_directory__/abacas.sh'
9 '$input_ref'
10 '$input_query'
11 '$ordered_contigs'
12 '$use_bin'
13 '$non'
14 '$append_bin'
15 '$out_bin'
16 '$out_crunch'
17 '$out_gaps'
18 '$out_fasta'
19 '$out_tab'
20 '$out_unused'
21 '$out_multi'
22 '$out_binmulti'
23 '$out_nonpseudo'
24 </command>
25 <inputs>
26 <param name="input_ref" type="data" format="fasta" label="Reference sequence" />
27 <param name="input_query" type="data" format="fasta" label="Sequence query file"/>
28 <param name="ordered_contigs" type="select" format="text" value="yes" label="Generate a multifasta file of the ordered contigs." help="The multifasta file of ordered contigs will be supplemental to the default pseudomolecule fasta file generated.">
29 <option value="yes">Yes</option>
30 <option value="no">No</option>
31 </param>
32 <param name="use_bin" type="select" format="text" value="yes" label="Generate a multifasta file of the unused contigs." help="The unsed contigs refer to contigs that were not used in the alignment.">
33 <option value="yes">Yes</option>
34 <option value="no">No</option>
35 </param>
36 <param name="non" type="select" format="text" value="yes" label="Generate a pseudomolecule by concatenating the aligned contigs without any nnn linkers." help="The no N's fasta file will be supplemental to the default pseudomolecule fasta file generated with n linkers.">
37 <option value="yes">Yes</option>
38 <option value="no">No</option>
39 </param>
40 <param name="append_bin" type="select" format="text" value="yes" label="Append the unused contigs from the bin onto the pseudomolecule." help="The pseudomolecule will be ordered and oriented and then any left over contigs from the bin will be concatenated to the end.">
41 <option value="yes">Yes</option>
42 <option value="no">No</option>
43 </param>
44 </inputs>
45 <outputs>
46 <data name="out_crunch" format="tabular" label="ACT crunch file"/>
47 <data name="out_tab" format="tabular" label="tab files"/>
48 <data name="out_gaps" format="tabular" label="gaps file"/>
49 <data name="out_fasta" format="tabular" label="pseudmolecule fasta file"/>
50 <data name="out_unused" format="tabular" label="unused contig information file"/>
51 <data name="out_bin" format="tabular" label="List of unused contigs"/>
52 <data name="out_multi" format="fasta" label="Multifasta file of contigs">
53 <filter>ordered_contigs=="yes"</filter>
54 </data>
55 <data name="out_binmulti" format="fasta" label="Multifasta file of bin contigs">
56 <filter>use_bin=="yes"</filter>
57 </data>
58 <data name="out_nonpseudo" format="fasta" label="Pseudomolecule with no N's">
59 <filter>non=="yes"</filter>
60 </data>
61 </outputs>
62 <tests>
63 <test>
64 <param name="input_ref" value="reference_sequence.fasta"/>
65 <param name="input_query" value="sequence_query.fasta"/>
66 <param name="ordered_contigs" value="no" />
67 <param name="use_bin" value="no" />
68 <param name="non" value="no" />
69 <param name="append_bin" value="no" />
70 <output name="out_crunch" value="out_crunch"/>
71 <output name="out_tab" value="out_tab"/>
72 <output name="out_gaps" value="out_gaps"/>
73 <output name="out_fasta" value="out_fasta"/>
74 <output name="out_unused" value="out_unused"/>
75 <output name="out_bin">
76 <assert_contents>
77 <has_text text ="NODE_1_length_1"/>
78 <has_text text ="NODE_2_length_10"/>
79 </assert_contents>
80 </output>
81 </test>
82 </tests>
83 <help>
84 <![CDATA[ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence]]>
85 </help>
86 <citations>
87 <citation type="bibtex">
88 @misc{sourceforgeABACAS,
89 title = {ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences},
90 publisher = {BioMalPar Consortium and Wellcome Trust Sanger Institute},
91 journal = {SourceForge},
92 url = {http://abacas.sourceforge.net/index.html},
93 }
94 </citation>
95 </citations>
96 </tool>