Mercurial > repos > nml > mob_suite
comparison mob_typer.xml @ 6:9424de64bfa8 draft
"planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
author | nml |
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date | Wed, 11 Dec 2019 19:17:11 -0500 |
parents | 09424ec94e80 |
children | 822575bf359f |
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5:09424ec94e80 | 6:9424de64bfa8 |
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1 <tool id="mob_typer" name="MOB-Typer" version="1.4.9.1+galaxy0"> | 1 <tool id="mob_typer" name="MOB-Typer" version="2.0.5+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 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.4.9.1">mob_suite</requirement> | 4 <requirement type="package" version="2.0.5">mob_suite</requirement> |
5 </requirements> | 5 </requirements> |
6 <version_command>mob_typer --version</version_command> | |
6 <command detect_errors="exit_code"> | 7 <command detect_errors="exit_code"> |
7 <![CDATA[ | 8 <![CDATA[ |
8 ln -s "${input}" "${input.name}"; | 9 ln -s '${input}' '${input.name}' && |
9 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" | 10 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile '${input.name}' |
11 ${host_range_detailed} | |
10 --min_rep_evalue '$adv_param.min_rep_evalue_value' | 12 --min_rep_evalue '$adv_param.min_rep_evalue_value' |
11 --min_mob_evalue '$adv_param.min_mob_evalue_value' | 13 --min_mob_evalue '$adv_param.min_mob_evalue_value' |
12 --min_con_evalue '$adv_param.min_con_evalue_value' | 14 --min_con_evalue '$adv_param.min_con_evalue_value' |
13 --min_ori_evalue '$adv_param.min_ori_evalue_value' | 15 --min_ori_evalue '$adv_param.min_ori_evalue_value' |
14 --min_mpf_evalue '$adv_param.min_mpf_evalue' | 16 --min_mpf_evalue '$adv_param.min_mpf_evalue' |
15 --min_rep_ident '$adv_param.min_rep_ident' | 17 --min_rep_ident '$adv_param.min_rep_ident' |
16 --min_mob_ident '$adv_param.min_mob_ident' | 18 --min_mob_ident '$adv_param.min_mob_ident' |
17 --min_ori_ident '$adv_param.min_ori_ident' | 19 --min_ori_ident '$adv_param.min_ori_ident' |
18 --min_mpf_ident '$adv_param.min_mpf_ident' | 20 --min_mpf_ident '$adv_param.min_mpf_ident' |
19 --outdir '.'; | 21 --outdir 'outdir'; |
20 ]]> | 22 ]]> |
21 </command> | 23 </command> |
22 <inputs> | 24 <inputs> |
23 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> | 25 <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" /> | |
24 <section name="adv_param" title="Advanced parameters" expanded="False"> | 27 <section name="adv_param" title="Advanced parameters" expanded="False"> |
25 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> | 28 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> |
26 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> | 29 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> |
27 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> | 30 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> |
28 <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements 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"/> |
29 <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/> | 32 <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/> |
30 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/> | 33 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/> |
31 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" 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"/> |
32 <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/> | 35 <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/> |
33 <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" 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"/> |
34 </section> | 37 </section> |
35 </inputs> | 38 </inputs> |
36 <outputs> | 39 <outputs> |
37 <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular"> | 40 <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" /> |
38 <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/> | 41 <data name="refseq_hostrange_phylogeny_tree" from_work_dir="outdir/*_refseqhostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Tree" format="newick"> |
39 </data> | 42 <filter>host_range_detailed</filter> |
43 </data> | |
44 <data name="literature_hostrange_phylogeny_tree" from_work_dir="outdir/*_literaturehostrange_phylogeny_tree.nwk" label="${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> | |
40 </outputs> | 62 </outputs> |
41 <tests> | 63 <tests> |
42 <test> | 64 <test> |
43 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> | 65 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> |
44 <assert_stdout> | 66 <param name="host_range_detailed" value="False" /> |
45 <has_text text="JN253636"/> | 67 <output name="plasmid_report"> |
46 </assert_stdout> | 68 <assert_contents> |
69 <has_text text="000145__HE610900_00001"/> | |
70 </assert_contents> | |
71 </output> | |
72 </test> | |
73 <test> | |
74 <param name="input" value="plasmid_476.fasta" ftype="fasta" /> | |
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"/> | |
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> | |
152 </output> | |
47 </test> | 153 </test> |
48 </tests> | 154 </tests> |
49 <help> | 155 <help> |
50 | 156 |
51 **Syntax** | 157 **Syntax** |