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comparison mob_hostrange.xml @ 41:cd69d25ce451 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit 96af868783fb62b932e49452133d3e1a8e1d181c-dirty"
author dfornika
date Thu, 14 Nov 2019 00:43:21 +0000
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40:8ad65c3af781 41:cd69d25ce451
1 <tool id="mob_hostrange" name="MOB-Hostrange" version="2.0.2+galaxy0">
2 <description>
3 Provides information on plasmid reproductive host range and transfer rate using both sequencing
4 and experimental data from public databases (NCBI) and publications (PubMED).
5 </description>
6 <requirements>
7 <requirement type="package" version="2.0.2">mob_suite</requirement>
8 </requirements>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 mob_hostrange
12 ${exact_match}
13 ${loose_match}
14 ${host_range_detailed}
15 #if str(${replicon_name}) != ""
16 --replicon_name '${replicon_name}'
17 #end if
18 #if str(${relaxase_name}) != ""
19 --relaxase_name '${relaxase_name}'
20 #end if
21 #if str(${relaxase_accession}) != ""
22 --relaxase_accession '${relaxase_accession}'
23 #end if
24 #if str(${cluster_id}) != ""
25 --cluster_id '${cluster_id}'
26 #end if
27 --inputseq "${inputseq}"
28 --outdir '.';
29 ]]>
30 </command>
31 <inputs>
32 <param name="inputseq" type="data" format="fasta" label="Input" help="plasmid FASTA file"/>
33 <param name="exact_match" type="boolean" truevalue="--exact_match" falsevalue="" checked="false"/>
34 <param name="loose_match" type="boolean" truevalue="--loose_match" falsevalue="" checked="false"/>
35 <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="false"/>
36 <param name="replicon_name" type="text" />
37 <param name="relaxase_name" type="text" />
38 <param name="relaxase_accession" type="text" />
39 <param name="cluster_id" type="text" />
40 </inputs>
41 <outputs>
42 <data name="hostrange_phylostats" label="${tool.name}: Phylostats report on ${input.name}" format="tabular">
43 <discover_datasets pattern=".+hostrange_phylostats\.txt" visible="true" format="tabular" />
44 </data>
45 <data name="hostrange_report" label="${tool.name}: Hostrange report on ${input.name}" format="tabular">
46 <discover_datasets pattern=".+hostrange_report\.txt" visible="true" format="tabular" />
47 </data>
48 </outputs>
49 <tests>
50 <test>
51 <param name="inputseq" value="plasmid_476.fasta" ftype="fasta"/>
52 <assert_stderr>
53 <has_text text="RefSeq Plasmid database found no hits"/>
54 </assert_stderr>
55 </test>
56 </tests>
57 <help>
58
59 **Syntax**
60
61 This tool provides information on plasmid reproductive host range and transfer rate using both sequencing and experimental data from public databases (NCBI) and publications (PubMED). The predicted host range represents a range of putative hosts where a given plasmid can stably replicate and be maintained by the host. The host range module makes no source attribution predictions of a plasmid.
62
63 For more information please visit https://github.com/phac-nml/mob-suite/.
64
65 -----
66
67 **Input:**
68
69 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
70
71
72 **Output:**
73
74 Tab-delimited reports listing predicted hostrange information. Refer to https://github.com/phac-nml/mob-suite#mob-hostrange-report-file-format for the description of each column.
75
76
77 </help>
78 <citations>
79 <citation type="bibtex">
80 @misc{githubmob-suite,
81 author = {Robertson J, Nash J},
82 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
83 publisher = {GitHub},
84 journal = {GitHub repository},
85 doi = {10.1099/mgen.0.000206},
86 url = {https://github.com/phac-nml/mob-suite}
87 }</citation>
88 </citations>
89 </tool>