comparison mob_recon.xml @ 0:820eec3fa31f draft

planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
author nml
date Thu, 24 May 2018 12:17:20 -0400
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children 2c419df5cdaa
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-1:000000000000 0:820eec3fa31f
1 <tool id="mob_recon" name="MOB-Recon" version="1.4.1">
2 <description>Type contigs and extract plasmid sequences</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_recon --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" --evalue '${adv_param.evalue}' --unicycler_contigs '${adv_param.unicycler_contigs}' --run_circlator '${adv_param.run_circlator}' --run_typer --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="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">
15 <option value="True">Yes</option>
16 <option value="False">No</option>
17 </param>
18 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
19 <option value="True">Yes</option>
20 <option value="False">No</option>
21 </param>
22
23 </section>
24 </inputs>
25 <outputs>
26 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name}: Overall contig MOB-recon report from ${input.name}"/>
27 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name}: Repetitive elements BLAST report from ${input.name}"/>
28 <data name="outfile3" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name}: Chromosomal sequences (if any) from ${input.name}"/>
29 <data name="outfile4" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name}: Aggregate MOB-typer report for all contigs from ${input.name}"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
34 <section name="adv_param">
35 <param name="evalue" value="0.00001"/>
36 <param name="unicycler_contigs" value="True"/>
37 <param name="run_circlator" value="True"/>
38 </section>
39 <output name="outfile1">
40 <assert_contents>
41 <has_text text="NC_019097"/>
42 </assert_contents>
43 </output>
44 </test>
45 </tests>
46 <help>
47
48 **Syntax**
49
50 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
51
52 For more information please visit https://github.com/phac-nml/mob-suite/.
53
54 -----
55
56 **Input:**
57
58 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
59
60
61 **Output:**
62
63 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.
64
65
66 </help>
67 <citations>
68 <citation type="bibtex">
69 @misc{githubmob-suite,
70 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
71 publisher = {GitHub},
72 journal = {GitHub repository},
73 url = {https://github.com/phac-nml/mob-suite},
74 }</citation>
75 </citations>
76 </tool>