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comparison mob_typer.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_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>