Mercurial > repos > nml > mob_suite
comparison mob_typer.xml @ 7:822575bf359f draft
"planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
author | nml |
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date | Fri, 05 Jun 2020 13:02:15 -0400 |
parents | 9424de64bfa8 |
children | 53f50adcb78e |
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6:9424de64bfa8 | 7:822575bf359f |
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1 <tool id="mob_typer" name="MOB-Typer" version="2.0.5+galaxy0"> | 1 <tool id="mob_typer" name="MOB-Typer" version="3.0.0"> |
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="2.0.5">mob_suite</requirement> | 4 <requirement type="package" version="3.0.0">mob_suite</requirement> |
5 </requirements> | 5 </requirements> |
6 <version_command>mob_typer --version</version_command> | 6 <version_command>mob_typer --version</version_command> |
7 <command detect_errors="exit_code"> | 7 <command detect_errors="exit_code"> |
8 <![CDATA[ | 8 <![CDATA[ |
9 ln -s '${input}' '${input.name}' && | 9 ln -s '${input}' '${input.name}' && |
10 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile '${input.name}' | 10 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile '${input.name}' |
11 ${host_range_detailed} | 11 |
12 | |
13 #if $adv_param.multi | |
14 --multi | |
15 #end if | |
16 | |
12 --min_rep_evalue '$adv_param.min_rep_evalue_value' | 17 --min_rep_evalue '$adv_param.min_rep_evalue_value' |
13 --min_mob_evalue '$adv_param.min_mob_evalue_value' | 18 --min_mob_evalue '$adv_param.min_mob_evalue_value' |
14 --min_con_evalue '$adv_param.min_con_evalue_value' | 19 --min_con_evalue '$adv_param.min_con_evalue_value' |
15 --min_ori_evalue '$adv_param.min_ori_evalue_value' | 20 --min_length '$adv_param.min_length' |
16 --min_mpf_evalue '$adv_param.min_mpf_evalue' | |
17 --min_rep_ident '$adv_param.min_rep_ident' | 21 --min_rep_ident '$adv_param.min_rep_ident' |
18 --min_mob_ident '$adv_param.min_mob_ident' | 22 --min_mob_ident '$adv_param.min_mob_ident' |
19 --min_ori_ident '$adv_param.min_ori_ident' | 23 |
20 --min_mpf_ident '$adv_param.min_mpf_ident' | 24 --min_con_ident '$adv_param.min_con_ident' |
21 --outdir 'outdir'; | 25 --min_rep_cov '$adv_param.min_rep_cov' |
26 --min_mob_cov '$adv_param.min_mob_cov' | |
27 --min_con_cov '$adv_param.min_con_cov' | |
28 --min_overlap '$adv_param.min_overlap' | |
29 | |
30 #if $adv_param.plasmid_db | |
31 --plasmid_db '$adv_param.plasmid_db' | |
32 #end if | |
33 | |
34 | |
35 #if $adv_param.plasmid_mash_db | |
36 --plasmid_mash_db '$adv_param.plasmid_mash_db' | |
37 #end if | |
38 | |
39 #if $adv_param.plasmid_meta | |
40 --plasmid_meta '$adv_param.plasmid_meta' | |
41 #end if | |
42 | |
43 #if $adv_param.repetitive_mask | |
44 --repetitive_mask '$adv_param.repetitive_mask' | |
45 #end if | |
46 | |
47 #if $adv_param.plasmid_mob | |
48 --plasmid_mob '$adv_param.plasmid_mob' | |
49 #end if | |
50 | |
51 #if $adv_param.plasmid_mpf | |
52 --plasmid_mpf '$adv_param.plasmid_mpf' | |
53 #end if | |
54 | |
55 #if $adv_param.plasmid_orit | |
56 --plasmid_orit '$adv_param.plasmid_orit' | |
57 #end if | |
58 | |
59 #if $adv_param.debug | |
60 --debug | |
61 #end if | |
62 | |
63 --out_file plasmid_report.txt; | |
64 | |
22 ]]> | 65 ]]> |
23 </command> | 66 </command> |
24 <inputs> | 67 <inputs> |
25 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> | 68 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> |
26 <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="true" label="Perform detailed host range analysis" /> | |
27 <section name="adv_param" title="Advanced parameters" expanded="False"> | 69 <section name="adv_param" title="Advanced parameters" expanded="False"> |
70 <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independant plasmid?" /> | |
28 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> | 71 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> |
29 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> | 72 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> |
30 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> | 73 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> |
31 <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements blastn"/> | 74 <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify"/> |
32 <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/> | |
33 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/> | 75 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/> |
34 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/> | 76 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/> |
35 <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/> | 77 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/> |
36 <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer" min="0" max="100" value="80"/> | 78 <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80"/> |
79 <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80"/> | |
80 <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"/> | |
81 <param name="min_overlap" label="Minimum overlap of fragments" type="integer" min="0" max="100" value="10"/> | |
82 <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" /> | |
83 <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help=""/> | |
84 <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="Companion MASH database of reference database"/> | |
85 <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"/> | |
86 <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="FASTA of plasmid replicons"/> | |
87 <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="FASTA of known repetitive elements"/> | |
88 <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="FASTA of plasmid relaxases"/> | |
89 <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"/> | |
90 <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"/> | |
37 </section> | 91 </section> |
38 </inputs> | 92 </inputs> |
39 <outputs> | 93 <outputs> |
40 <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" /> | 94 <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" /> |
41 <data name="refseq_hostrange_phylogeny_tree" from_work_dir="outdir/*_refseqhostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Tree" format="newick"> | |
42 <filter>host_range_detailed</filter> | |
43 </data> | |
44 <data name="literature_hostrange_phylogeny_tree" from_work_dir="outdir/*_literaturehostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: Literature Host Range Phylogeny Tree" format="newick"> | |
45 <filter>host_range_detailed</filter> | |
46 </data> | |
47 <data name="refseq_hostrange_ascii_tree" from_work_dir="outdir/*_refseqhostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range ASCII Tree" format="txt"> | |
48 <filter>host_range_detailed</filter> | |
49 </data> | |
50 <data name="literature_hostrange_ascii_tree" from_work_dir="outdir/*_literaturehostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: Literature Host Range ASCII Tree" format="txt"> | |
51 <filter>host_range_detailed</filter> | |
52 </data> | |
53 <data name="literature_report" from_work_dir="outdir/*_literature_report.txt" label="${tool.name} on ${input.element_identifier}: Literature Report" format="tabular"> | |
54 <filter>host_range_detailed</filter> | |
55 </data> | |
56 <data name="refseq_hostrange_report" from_work_dir="outdir/*_refseqhostrange_report.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Report" format="tabular"> | |
57 <filter>host_range_detailed</filter> | |
58 </data> | |
59 <data name="refseq_hostrange_phylostats" from_work_dir="outdir/*_refseqhostrange_phylostats.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Stats" format="tabular"> | |
60 <filter>host_range_detailed</filter> | |
61 </data> | |
62 </outputs> | 95 </outputs> |
63 <tests> | 96 <tests> |
64 <test> | 97 <test> |
65 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> | 98 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> |
66 <param name="host_range_detailed" value="False" /> | |
67 <output name="plasmid_report"> | 99 <output name="plasmid_report"> |
68 <assert_contents> | 100 <assert_contents> |
69 <has_text text="000145__HE610900_00001"/> | 101 <has_text text="KJ484639"/> |
70 </assert_contents> | 102 <has_text text="MOBP"/> |
71 </output> | 103 <has_text text="NC_019097"/> |
72 </test> | 104 <has_text text="conjugative"/> |
73 <test> | 105 <has_text text="AA474"/> |
74 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> | 106 <has_text text="AI614"/> |
75 <param name="host_range_detailed" value="True" /> | |
76 <output name="refseq_hostrange_phylogeny_tree"> | |
77 <assert_contents> | |
78 <has_text text="(624:1,984897:1)"/> | |
79 </assert_contents> | |
80 </output> | |
81 </test> | |
82 <test> | |
83 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> | |
84 <param name="host_range_detailed" value="True" /> | |
85 <output name="literature_hostrange_phylogeny_tree"> | |
86 <assert_contents> | |
87 <has_text text="(90371:1,611:1,28144:1)"/> | |
88 </assert_contents> | |
89 </output> | |
90 </test> | |
91 <test> | |
92 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> | |
93 <param name="host_range_detailed" value="True" /> | |
94 <output name="refseq_hostrange_ascii_tree"> | |
95 <assert_contents> | |
96 <has_text text="order, Enterobacterales"/> | |
97 <has_text text="family, Enterobacteriaceae"/> | |
98 <has_text text="genus, Shigella"/> | |
99 <has_text text="species, Escherichia coli"/> | |
100 <has_text text="genus, Serratia"/> | |
101 <has_text text="species, Serratia marcescens"/> | |
102 <has_text text="species, Klebsiella pneumoniae"/> | |
103 </assert_contents> | |
104 </output> | |
105 </test> | |
106 <test> | |
107 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> | |
108 <param name="host_range_detailed" value="True" /> | |
109 <output name="literature_hostrange_ascii_tree"> | |
110 <assert_contents> | |
111 <has_text text="family, Enterobacteriaceae"/> | |
112 <has_text text="species, Escherichia coli"/> | |
113 <has_text text="species, Klebsiella pneumoniae"/> | |
114 <has_text text="subspecies, Salmonella enterica subsp. enterica"/> | |
115 </assert_contents> | |
116 </output> | |
117 </test> | |
118 <test> | |
119 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> | |
120 <param name="host_range_detailed" value="True" /> | |
121 <output name="literature_report"> | |
122 <assert_contents> | |
123 <has_text text="IncI1"/> | |
124 <has_text text="R64"/> | |
125 <has_text text="pHNRD174"/> | |
126 <has_text text="pKHSB1"/> | |
127 <has_text text="pCTXM1-MU2"/> | |
128 <has_text_matching expression="family\tEnterobacteriaceae"/> | 107 <has_text_matching expression="family\tEnterobacteriaceae"/> |
129 <has_text_matching expression="order\tEnterobacteriales"/> | |
130 </assert_contents> | |
131 </output> | |
132 </test> | |
133 <test> | |
134 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> | |
135 <param name="host_range_detailed" value="True" /> | |
136 <output name="refseq_hostrange_report"> | |
137 <assert_contents> | |
138 <has_text text="IncI1"/> | |
139 <has_text text="Enterobacterales"/> | |
140 </assert_contents> | |
141 </output> | |
142 </test> | |
143 <test> | |
144 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> | |
145 <param name="host_range_detailed" value="True" /> | |
146 <output name="refseq_hostrange_phylostats"> | |
147 <assert_contents> | |
148 <has_line_matching expression="rank\tsci_name\tdb_hits\tconvergance_rank\tconvergance_sci_name"/> | |
149 <has_line_matching expression="family\tEnterobacteriaceae\t351"/> | |
150 <has_line_matching expression="genus\tSalmonella\t113"/> | |
151 </assert_contents> | 108 </assert_contents> |
152 </output> | 109 </output> |
153 </test> | 110 </test> |
154 </tests> | 111 </tests> |
155 <help> | 112 <help> |