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comparison mob_recon.xml @ 1:2c419df5cdaa draft

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planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
author nml
date Thu, 26 Jul 2018 14:50:59 -0400
parents 820eec3fa31f
children 2c7f721a4905
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0:820eec3fa31f 1:2c419df5cdaa
1 <tool id="mob_recon" name="MOB-Recon" version="1.4.1"> 1 <tool id="mob_recon" name="MOB-Recon" version="1.4.5">
2 <description>Type contigs and extract plasmid sequences</description> 2 <description>Type contigs and extract plasmid sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4.1">mob_suite</requirement> 4 <requirement type="package" version="1.4.5">mob_suite</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
7 ln -s "${input}" "${input.name}"; 7 <![CDATA[
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 '.'; 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 ]]>
9 </command> 22 </command>
10 <inputs> 23 <inputs>
11 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> 24 <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"> 25 <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"> 26 <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> 27 <option value="True">Yes</option>
16 <option value="False">No</option> 28 <option value="False">No</option>
17 </param> 29 </param>
18 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True"> 30 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
19 <option value="True">Yes</option> 31 <option value="True">Yes</option>
20 <option value="False">No</option> 32 <option value="False">No</option>
21 </param> 33 </param>
22 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>
23 </section> 44 </section>
24 </inputs> 45 </inputs>
25 <outputs> 46 <outputs>
26 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name}: Overall contig MOB-recon report from ${input.name}"/> 47 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name}: Overall contig MOB-recon report"/>
27 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name}: Repetitive elements BLAST report from ${input.name}"/> 48 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name}: Repetitive elements BLAST report"/>
28 <data name="outfile3" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name}: Chromosomal sequences (if any) from ${input.name}"/> 49 <data name="outfile3" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name}: Chromosomal sequences"/>
29 <data name="outfile4" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name}: Aggregate MOB-typer report for all contigs from ${input.name}"/> 50 <data name="outfile4" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${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="true" assign_primary_output="false"/>
53 </data>
30 </outputs> 54 </outputs>
31 <tests> 55 <tests>
32 <test> 56 <test>
33 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> 57 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
34 <section name="adv_param"> 58 <section name="adv_param">
60 84
61 **Output:** 85 **Output:**
62 86
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. 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.
64 88
89 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
90
65 91
66 </help> 92 </help>
67 <citations> 93 <citations>
68 <citation type="bibtex"> 94 <citation type="bibtex">
69 @misc{githubmob-suite, 95 @misc{githubmob-suite,
96 author = {Robertson J, Nash J},
70 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.}, 97 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
71 publisher = {GitHub}, 98 publisher = {GitHub},
72 journal = {GitHub repository}, 99 journal = {GitHub repository},
73 url = {https://github.com/phac-nml/mob-suite}, 100 doi = {10.1099/mgen.0.000206},
101 url = {https://github.com/phac-nml/mob-suite}
74 }</citation> 102 }</citation>
75 </citations> 103 </citations>
76 </tool> 104 </tool>