Mercurial > repos > nml > mob_suite
comparison mob_typer.xml @ 1:2c419df5cdaa draft
planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
author | nml |
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date | Thu, 26 Jul 2018 14:50:59 -0400 |
parents | 820eec3fa31f |
children | 2c7f721a4905 |
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0:820eec3fa31f | 1:2c419df5cdaa |
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1 <tool id="mob_typer" name="MOB-Typer" version="1.4.1"> | 1 <tool id="mob_typer" name="MOB-Typer" version="1.4.5"> |
2 <description>Get the plasmid type and mobility given its sequence</description> | 2 <description>Get the plasmid type and mobility given its sequence</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 <![CDATA[ | |
7 ln -s "${input}" "${input.name}"; | 8 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 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" |
10 #if str($adv_param.min_rep_evalue_condition.min_rep_evalue_param) == "True": | |
11 --min_rep_evalue $adv_param.min_rep_evalue_condition.min_rep_evalue_value | |
12 #end if | |
13 #if str($adv_param.min_mob_evalue_condition.min_mob_evalue_param) == "True": | |
14 --min_mob_evalue $adv_param.min_mob_evalue_condition.min_mob_evalue_value | |
15 #end if | |
16 #if str($adv_param.min_con_evalue_condition.min_con_evalue_param) == "True": | |
17 --min_con_evalue $adv_param.min_con_evalue_condition.min_con_evalue_value | |
18 #end if | |
19 #if str($adv_param.min_ori_evalue_condition.min_ori_evalue_param) == "True": | |
20 --min_ori_evalue $adv_param.min_ori_evalue_condition.min_ori_evalue_value | |
21 #end if | |
22 --outdir '.'; | |
23 ]]> | |
9 </command> | 24 </command> |
10 <inputs> | 25 <inputs> |
11 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> | 26 <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"> | 27 <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"/> | 28 <conditional name="min_rep_evalue_condition"> |
14 <param name="min_ident" label="Minimum sequence identity for BLAST" type="float" min="1" max="100" value="80"/> | 29 <param name="min_rep_evalue_param" label="Minimum evalue threshold for replicon blastn" type="select" value="False"> |
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"/> | 30 <option value="False">No</option> |
31 <option value="True">Yes</option> | |
32 </param> | |
33 <when value="True"> | |
34 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> | |
35 </when> | |
36 <when value="False"/> | |
37 </conditional> | |
38 <conditional name="min_mob_evalue_condition"> | |
39 <param name="min_mob_evalue_param" label="Minimum evalue threshold for relaxase tblastn" type="select" value="False"> | |
40 <option value="False">No</option> | |
41 <option value="True">Yes</option> | |
42 </param> | |
43 <when value="True"> | |
44 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="e-value (default: 0.00001)"/> | |
45 </when> | |
46 <when value="False"/> | |
47 </conditional> | |
48 <conditional name="min_con_evalue_condition"> | |
49 <param name="min_con_evalue_param" label="Minimum evalue threshold for contig blastn" type="select" value="False"> | |
50 <option value="False">No</option> | |
51 <option value="True">Yes</option> | |
52 </param> | |
53 <when value="True"> | |
54 <param name="min_con_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> | |
55 </when> | |
56 <when value="False"/> | |
57 </conditional> | |
58 <conditional name="min_ori_evalue_condition"> | |
59 <param name="min_ori_evalue_param" label="Minimum evalue threshold for oriT elements blastn" type="select" value="False"> | |
60 <option value="False">No</option> | |
61 <option value="True">Yes</option> | |
62 </param> | |
63 <when value="True"> | |
64 <param name="min_ori_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> | |
65 </when> | |
66 <when value="False"/> | |
67 </conditional> | |
16 </section> | 68 </section> |
17 </inputs> | 69 </inputs> |
18 <outputs> | 70 <outputs> |
19 <data name="outfile1" label="${tool.name}: Report from ${input.name}" format="tabular" hidden="false"> | 71 <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular"> |
20 <discover_datasets pattern=".+_report\.txt" visible="true" ext="tabular" assign_primary_output="true"/> | 72 <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/> |
21 </data> | 73 </data> |
22 </outputs> | 74 </outputs> |
23 <tests> | 75 <tests> |
24 <test> | 76 <test> |
25 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> | 77 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> |
50 | 102 |
51 </help> | 103 </help> |
52 <citations> | 104 <citations> |
53 <citation type="bibtex"> | 105 <citation type="bibtex"> |
54 @misc{githubmob-suite, | 106 @misc{githubmob-suite, |
107 author = {Robertson J, Nash J}, | |
55 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.}, | 108 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.}, |
56 publisher = {GitHub}, | 109 publisher = {GitHub}, |
57 journal = {GitHub repository}, | 110 journal = {GitHub repository}, |
58 url = {https://github.com/phac-nml/mob-suite}, | 111 doi = {10.1099/mgen.0.000206}, |
112 url = {https://github.com/phac-nml/mob-suite} | |
59 }</citation> | 113 }</citation> |
60 </citations> | 114 </citations> |
61 </tool> | 115 </tool> |