Mercurial > repos > nml > mob_suite
comparison mob_typer.xml @ 0:820eec3fa31f draft
planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
author | nml |
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date | Thu, 24 May 2018 12:17:20 -0400 |
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children | 2c419df5cdaa |
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1 <tool id="mob_typer" name="MOB-Typer" version="1.4.1"> | |
2 <description>Get the plasmid type and mobility given its sequence</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.4.1">mob_suite</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"> | |
7 ln -s "${input}" "${input.name}"; | |
8 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" --evalue '${adv_param.evalue}' --min_ident '${adv_param.min_ident}' --min_cov '${adv_param.min_cov}' --outdir '.'; | |
9 </command> | |
10 <inputs> | |
11 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> | |
12 <section name="adv_param" title="Advanced parameters" expanded="False"> | |
13 <param name="evalue" label="Minimum e-value threshold for BLAST" type="float" min="0.000000000000000000001" max="1" value="0.00001"/> | |
14 <param name="min_ident" label="Minimum sequence identity for BLAST" type="float" min="1" max="100" value="80"/> | |
15 <param name="min_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="float" min="1" max="100" value="65"/> | |
16 </section> | |
17 </inputs> | |
18 <outputs> | |
19 <data name="outfile1" label="${tool.name}: Report from ${input.name}" format="tabular" hidden="false"> | |
20 <discover_datasets pattern=".+_report\.txt" visible="true" ext="tabular" assign_primary_output="true"/> | |
21 </data> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> | |
26 <assert_stdout> | |
27 <has_text text="JN253636"/> | |
28 </assert_stdout> | |
29 </test> | |
30 </tests> | |
31 <help> | |
32 | |
33 **Syntax** | |
34 | |
35 This tool provides *in-silico* predictions on plasmid typing including identification of replicon, relaxase and mate-pair formation protein types. MOB-typer also predicts mobility of a plasmid (Conjugative, Mobilizable, Non-mobilizable). Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single plasmid. | |
36 | |
37 For more information please visit https://github.com/phac-nml/mob-suite/. | |
38 | |
39 ----- | |
40 | |
41 **Input:** | |
42 | |
43 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta): | |
44 | |
45 | |
46 **Output:** | |
47 | |
48 Tab-delimited report listing identified plasmid(s) and their predicted mobility. Refer to https://github.com/phac-nml/mob-suite#mob-typer-report-file-format for the description of each column. | |
49 | |
50 | |
51 </help> | |
52 <citations> | |
53 <citation type="bibtex"> | |
54 @misc{githubmob-suite, | |
55 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.}, | |
56 publisher = {GitHub}, | |
57 journal = {GitHub repository}, | |
58 url = {https://github.com/phac-nml/mob-suite}, | |
59 }</citation> | |
60 </citations> | |
61 </tool> |