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comparison mob_recon.xml @ 7:822575bf359f draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
author nml
date Fri, 05 Jun 2020 13:02:15 -0400
parents 9424de64bfa8
children 53f50adcb78e
comparison
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6:9424de64bfa8 7:822575bf359f
1 <tool id="mob_recon" name="MOB-Recon" version="2.0.5+galaxy0"> 1 <tool id="mob_recon" name="MOB-Recon" version="3.0.0">
2 <description>Type contigs and extract plasmid sequences</description> 2 <description>Type contigs and extract plasmid sequences</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_recon --version</version_command> 6 <version_command>mob_recon --version</version_command>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9 #import re 9 #import re
10 #import os.path 10 #import os.path
11 11
12 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta') 12 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta')
13 ln -s '$input' '$named_input' && 13 ln -s '$input' '$named_input' &&
14 14
15 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile '${named_input}' 15
16 #if str($adv_param.unicycler_contigs) == "True": 16 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile '${named_input}' --run_typer
17
18 #if $adv_param.unicycler_contigs:
17 --unicycler_contigs 19 --unicycler_contigs
18 #end if 20 #end if
19 #if str($adv_param.run_circlator) == "True": 21
20 --run_circlator 22 #if $adv_param.run_overhang:
23 --run_overhang
21 #end if 24 #end if
22 #if str($adv_param.min_length_condition.min_length_param) == "True": 25
23 --min_length '${adv_param.min_length_condition.min_length_value}' 26 #if $adv_param.debug:
24 #end if 27 --debug
25 --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}' 28 #end if
29
30 #if $adv_param.plasmid_db
31 --plasmid_db '$adv_param.plasmid_db'
32 #end if
33
34 #if $adv_param.plasmid_mash_db
35 --plasmid_mash_db '$adv_param.plasmid_mash_db'
36 #end if
37
38 #if $adv_param.plasmid_meta
39 --plasmid_meta '$adv_param.plasmid_meta'
40 #end if
41
42 #if $adv_param.repetitive_mask
43 --repetitive_mask '$adv_param.repetitive_mask'
44 #end if
45
46 #if $adv_param.plasmid_mob
47 --plasmid_mob '$adv_param.plasmid_mob'
48 #end if
49
50 #if $adv_param.plasmid_mpf
51 --plasmid_mpf '$adv_param.plasmid_mpf'
52 #end if
53
54 #if $adv_param.plasmid_orit
55 --plasmid_orit '$adv_param.plasmid_orit'
56 #end if
57
58 --min_length '${adv_param.min_length}'
59 --min_rep_evalue '${adv_param.min_rep_evalue}'
26 --min_rep_evalue '${adv_param.min_rep_evalue}' 60 --min_rep_evalue '${adv_param.min_rep_evalue}'
27 --min_mob_evalue '${adv_param.min_mob_evalue}' 61 --min_mob_evalue '${adv_param.min_mob_evalue}'
28 --min_con_evalue '${adv_param.min_con_evalue}' 62 --min_con_evalue '${adv_param.min_con_evalue}'
29 --min_rep_ident '${adv_param.min_rep_ident}' 63 --min_rep_ident '${adv_param.min_rep_ident}'
30 --min_mob_ident '${adv_param.min_mob_ident}' 64 --min_mob_ident '${adv_param.min_mob_ident}'
31 --min_con_ident '${adv_param.min_con_ident}' 65 --min_con_ident '${adv_param.min_con_ident}'
32 --min_rpp_ident '${adv_param.min_rpp_ident}' 66 --min_rpp_ident '${adv_param.min_rpp_ident}'
67
68 --min_rep_cov '${adv_param.min_rep_cov}'
69 --min_mob_cov '${adv_param.min_mob_cov}'
70 --min_con_cov '${adv_param.min_con_cov}'
71 --min_rpp_cov '${adv_param.min_rpp_cov}'
33 --outdir 'outdir' && 72 --outdir 'outdir' &&
34 mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true) 73 mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true)
35 ]]> 74 ]]>
36 </command> 75 </command>
37 <inputs> 76 <inputs>
38 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> 77 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
39 <section name="adv_param" title="Advanced parameters" expanded="False"> 78 <section name="adv_param" title="Advanced parameters" expanded="False">
40 <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True"> 79 <param name="unicycler_contigs" type="boolean" truevalue="true" falsevalue="" checked="true" label="Check for circularity flag generated by unicycler in contigs fasta headers?"/>
41 <option value="True">Yes</option> 80 <param name="run_overhang" type="boolean" truevalue="true" falsevalue="" checked="true" label="Detect circular contigs (i.e. potential plasmids) with assembly overhangs?"/>
42 <option value="False">No</option> 81 <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?"/>
43 </param> 82
44 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
45 <option value="True">Yes</option>
46 <option value="False">No</option>
47 </param>
48 <conditional name="min_length_condition">
49 <param name="min_length_param" label="Minimum length of contigs to process" 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_length_value" type="integer" value="500" min="50"/>
55 </when>
56 <when value="False"/>
57 </conditional>
58 <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001"/> 83 <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001"/>
59 <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float" min="0.00001" max="1" value="0.00001"/> 84 <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float" min="0.00001" max="1" value="0.00001"/>
60 <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float" min="0.00001" max="1" value="0.00001"/> 85 <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float" min="0.00001" max="1" value="0.00001"/>
61 <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float" min="0.00001" max="1" value="0.00001"/> 86 <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float" min="0.00001" max="1" value="0.00001"/>
87 <param name="min_length" label="Minimum length of contigs to classify" type="integer" value="1000"/>
62 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/> 88 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>
63 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/> 89 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>
64 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/> 90 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/>
65 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/> 91 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/>
92
93 <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80"/>
94 <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80"/>
95 <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="60"/>
96 <param name="min_rpp_cov" label="Minimum percentage coverage of contigs by repetitive elements" type="integer" min="0" max="100" value="80"/>
97
98 <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help=""/>
99 <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="MASH sketch of the reference plasmids database"/>
100 <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help=""/>
101 <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help=""/>
102 <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help=""/>
103 <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help=""/>
104 <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help=""/>
105 <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help=""/>
66 </section> 106 </section>
67 </inputs> 107 </inputs>
68 <outputs> 108 <outputs>
69 <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/> 109 <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/>
70 <data name="repetitive_blast_report" format="tabular" from_work_dir="outdir/repetitive_blast_report.txt" label="${tool.name} on ${input.element_identifier}: Repetitive elements BLAST report"/> 110 <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_results.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/>
71 <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_aggregate_report.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/>
72 <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: Chromosomal sequences"/> 111 <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: Chromosomal sequences"/>
73 <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: Plasmids"> 112 <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: Plasmids">
74 <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" /> 113 <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" />
75 </collection> 114 </collection>
76 </outputs> 115 </outputs>
77 <tests> 116 <tests>
78 <test> 117 <test>
79 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> 118 <param name="input" value="Ecoli_strain_KV7_complete_LT795502.fasta" ftype="fasta"/>
80 <section name="adv_param"> 119 <section name="adv_param">
81 <param name="unicycler_contigs" value="True"/> 120 <param name="unicycler_contigs" value="True"/>
82 <param name="run_circlator" value="True"/> 121 <param name="run_overhang" value="True"/>
83 </section> 122 </section>
84 <output name="contig_report"> 123 <output name="contig_report">
85 <assert_contents> 124 <assert_contents>
86 <has_text text="NC_019097"/> 125 <has_text text="chromosome"/>
126 <has_text text="plasmid"/>
127 <has_text text="IncHI1A"/>
128 <has_text text="IncN"/>
129 </assert_contents>
130 </output>
131 <output name="mobtyper_aggregate_report">
132 <assert_contents>
133 <has_text text="conjugative"/>
134 <has_text text="Gammaproteobacteria"/>
135 <has_text text="223020"/>
87 </assert_contents> 136 </assert_contents>
88 </output> 137 </output>
89 </test> 138 </test>
90 </tests> 139 </tests>
91 <help> 140 <help>