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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite commit 8bd2d0ff4101e7e7e6a45247d616929593a03cd4
author nml
date Fri, 21 Feb 2025 18:41:14 +0000
parents 53f50adcb78e
children
comparison
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9:93ba63eaf394 10:2fd93022d5d7
1 <tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy0"> 1 <tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy0">
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 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <version_command>mob_typer --version</version_command> 8 <version_command>mob_typer --version</version_command>
8 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
9 <![CDATA[ 10 <![CDATA[
10 ln -s '${input}' '${input.name}' && 11 ln -s '${input}' '${input.name}' &&
58 #end if 59 #end if
59 60
60 #if $adv_param.debug 61 #if $adv_param.debug
61 --debug 62 --debug
62 #end if 63 #end if
64
65 #if $adv_param.biomarker_report_file
66 --biomarker_report_file biomarker_report.txt
67 #end if
68
63 69
64 --out_file plasmid_report.txt; 70 --out_file plasmid_report.txt;
65 71
66 ]]> 72 ]]>
67 </command> 73 </command>
68 <inputs> 74 <inputs>
69 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> 75 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
70 <section name="adv_param" title="Advanced parameters" expanded="False"> 76 <section name="adv_param" title="Advanced parameters" expanded="False">
71 <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independant plasmid?" /> 77 <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independent plasmid?" help="Treat each sequence in the FASTA file as a separate input (--multi)" />
72 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> 78 <param name="biomarker_report_file" type="boolean" truevalue="true" falsevalue="" checked="false" label="Output BLAST biomarker report?" help="The report will report all biomarkers identified in a given query plasmid (--biomarker_report_file)" />
73 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> 79
74 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> 80 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn" help="(--min_rep_evalue)"/>
75 <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify"/> 81 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn" help="(--min_mob_evalue)"/>
76 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/> 82 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn" help="(--min_con_evalue)"/>
77 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/> 83 <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify (bp)" help="(--min_length)"/>
78 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/> 84 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80" help="(--min_rep_ident)"/>
79 <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80"/> 85 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80" help="(--min_mob_ident)"/>
80 <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80"/> 86 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80" help="(--min_con_ident)"/>
81 <param name="min_con_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="integer" min="0" max="100" value="70"/> 87 <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80" help="(--min_rep_ident)"/>
82 <param name="min_overlap" label="Minimum overlap of fragments" type="integer" min="0" max="100" value="10"/> 88 <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80" help="(--min_mob_cov)"/>
83 <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" /> 89 <param name="min_con_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="integer" min="0" max="100" value="70" help="(--min_con_cov)"/>
84 <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help=""/> 90 <param name="min_overlap" label="Minimum overlap of fragments (bp)" type="integer" min="0" max="100" value="10" help="(--min_overlap)"/>
85 <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="Companion MASH database of reference database"/> 91 <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" help="(--debug)"/>
86 <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="MOB-cluster plasmid cluster formatted metadata file matched to the reference plasmid db"/> 92 <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help="(--plasmid_db)"/>
87 <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="FASTA of plasmid replicons"/> 93 <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="Custom MASH plasmid reference database (--plasmid_mash_db)"/>
88 <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="FASTA of known repetitive elements"/> 94 <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="MOB-cluster plasmid cluster formatted metadata file matched to the reference plasmid database (--plasmid_meta)"/>
89 <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="FASTA of plasmid relaxases"/> 95 <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="FASTA of plasmid replicons custom database (--plasmid_replicons)"/>
90 <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="FASTA of known plasmid mate-pair proteins"/> 96 <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="FASTA of known repetitive elements custom database (--repetitive_mask)"/>
91 <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT dna sequences"/> 97 <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="FASTA of plasmid relaxases custom database (--plasmid_mob)"/>
98 <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="FASTA of known plasmid mate-pair proteins custom database (--plasmid_mpf)"/>
99 <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT DNA sequences custom database (--plasmid_orit)"/>
92 </section> 100 </section>
93 </inputs> 101 </inputs>
94 <outputs> 102 <outputs>
95 <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" /> 103 <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" />
104 <data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}" format="tabular" />
96 </outputs> 105 </outputs>
97 <tests> 106 <tests>
98 <test> 107 <test>
99 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> 108 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
100 <output name="plasmid_report"> 109 <output name="plasmid_report">
112 </tests> 121 </tests>
113 <help> 122 <help>
114 123
115 **Syntax** 124 **Syntax**
116 125
117 This tool provides *in-silico* predictions on plasmid typing including identification of replicon, relaxase and mate-pair formation protein types. MOB-typer also predicts mobility of a plasmid (Conjugative, Mobilizable, Non-mobilizable). Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single plasmid. 126 This tool provides *in silico* predictions on plasmid typing including identification of replicon, relaxase and mate-pair formation protein types. MOB-typer also predicts mobility of a plasmid (Conjugative, Mobilizable, Non-mobilizable) and potential host range.
118 127
119 For more information please visit https://github.com/phac-nml/mob-suite/. 128 For more information please visit https://github.com/phac-nml/mob-suite/.
120 129
121 ----- 130 -----
122 131
125 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta): 134 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
126 135
127 136
128 **Output:** 137 **Output:**
129 138
130 Tab-delimited report listing identified plasmid(s) and their predicted mobility. Refer to https://github.com/phac-nml/mob-suite#mob-typer-report-file-format for the description of each column. 139 Tab-delimited report listing identified plasmid(s) and their predicted mobility and host range and optionally a biomarker report (if selected). Refer to https://github.com/phac-nml/mob-suite#mob-typer-report-file-format for the description of each column.
131 140
132 141 **Note:** Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single plasmid or turn on the **--multi** parameter (i.e. *Treat each input sequence as an independent plasmid?*).
133 </help> 142 </help>
134 <citations> 143 <citations>
135 <citation type="bibtex"> 144 <citation type="bibtex">
136 @misc{githubmob-suite, 145 @misc{githubmob-suite,
137 author = {Robertson J, Nash J}, 146 author = {Robertson J, Nash J},