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comparison cpo_mobsuite.xml @ 1:fea89c4d5227 draft

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author jjjjia
date Thu, 16 Aug 2018 19:27:05 -0400
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0:917a05a03ac9 1:fea89c4d5227
1 <tool id="mob_recon" name="MOB-Recon" version="1.4.8">
2 <description>Type contigs and extract plasmid sequences</description>
3 <requirements>
4 <requirement type="package" version="1.4.8">mob_suite</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8 ln -s "${input}" "${input.name}";
9
10 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}"
11 #if str($adv_param.unicycler_contigs) == "True":
12 --unicycler_contigs
13 #end if
14 #if str($adv_param.run_circlator) == "True":
15 --run_circlator
16 #end if
17 #if str($adv_param.min_length_condition.min_length_param) == "True":
18 --min_length ${adv_param.min_length_condition.min_length_value}
19 #end if
20 --run_typer --outdir '.';
21 ]]>
22 </command>
23 <inputs>
24 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
25 <section name="adv_param" title="Advanced parameters" expanded="False">
26 <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">
27 <option value="True">Yes</option>
28 <option value="False">No</option>
29 </param>
30 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
31 <option value="True">Yes</option>
32 <option value="False">No</option>
33 </param>
34 <conditional name="min_length_condition">
35 <param name="min_length_param" label="Minimum length of contigs to classify" type="select" value="False">
36 <option value="False">No</option>
37 <option value="True">Yes</option>
38 </param>
39 <when value="True">
40 <param name="min_length_value" type="integer" value="500" min="50"/>
41 </when>
42 <when value="False"/>
43 </conditional>
44 </section>
45 </inputs>
46 <outputs>
47 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name}: Overall contig MOB-recon report"/>
48 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name}: Repetitive elements BLAST report"/>
49 <data name="outfile3" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name}: Chromosomal sequences"/>
50 <data name="outfile4" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name}: Aggregate MOB-typer report for all contigs"/>
51 <data name="outfile5" format="fasta" label="${tool.name}: Plasmid sequence" hidden="true">
52 <discover_datasets pattern="plasmid_.+\.(?P&lt;ext&gt;.+)" ext="fasta" visible="false" assign_primary_output="false"/>
53 </data>
54 </outputs>
55 <tests>
56 <test>
57 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
58 <section name="adv_param">
59 <param name="evalue" value="0.00001"/>
60 <param name="unicycler_contigs" value="True"/>
61 <param name="run_circlator" value="True"/>
62 </section>
63 <output name="outfile1">
64 <assert_contents>
65 <has_text text="NC_019097"/>
66 </assert_contents>
67 </output>
68 </test>
69 </tests>
70 <help>
71
72 **Syntax**
73
74 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
75
76 For more information please visit https://github.com/phac-nml/mob-suite/.
77
78 -----
79
80 **Input:**
81
82 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
83
84
85 **Output:**
86
87 Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column.
88
89 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
90
91
92 </help>
93 <citations>
94 <citation type="bibtex">
95 @misc{githubmob-suite,
96 author = {Robertson J, Nash J},
97 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
98 publisher = {GitHub},
99 journal = {GitHub repository},
100 doi = {10.1099/mgen.0.000206},
101 url = {https://github.com/phac-nml/mob-suite}
102 }</citation>
103 </citations>
104 </tool>