annotate mob_recon.xml @ 9:93ba63eaf394 draft default tip

"planemo upload for repository https://github.com/phac-nml/mob-suite commit 7ecd5079d62ccc38a9cc41bd2b9553b21221c76a"
author nml
date Thu, 05 Aug 2021 21:53:36 +0000
parents 53f50adcb78e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
53f50adcb78e "planemo upload for repository https://github.com/phac-nml/mob-suite commit 314c26f1f5e22511c6f406cd9b7108f873cec295"
nml
parents: 7
diff changeset
1 <tool id="mob_recon" name="MOB-Recon" version="@VERSION@+galaxy0">
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
2 <description>Type contigs and extract plasmid sequences</description>
8
53f50adcb78e "planemo upload for repository https://github.com/phac-nml/mob-suite commit 314c26f1f5e22511c6f406cd9b7108f873cec295"
nml
parents: 7
diff changeset
3 <macros>
53f50adcb78e "planemo upload for repository https://github.com/phac-nml/mob-suite commit 314c26f1f5e22511c6f406cd9b7108f873cec295"
nml
parents: 7
diff changeset
4 <import>macros.xml</import>
53f50adcb78e "planemo upload for repository https://github.com/phac-nml/mob-suite commit 314c26f1f5e22511c6f406cd9b7108f873cec295"
nml
parents: 7
diff changeset
5 </macros>
53f50adcb78e "planemo upload for repository https://github.com/phac-nml/mob-suite commit 314c26f1f5e22511c6f406cd9b7108f873cec295"
nml
parents: 7
diff changeset
6 <expand macro="requirements" />
6
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
7 <version_command>mob_recon --version</version_command>
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
8 <command detect_errors="exit_code">
1
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
9 <![CDATA[
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
10 #import re
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
11 #import os.path
1
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
12
6
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
13 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta')
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
14 ln -s '$input' '$named_input' &&
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
15
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
16
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
17 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile '${named_input}' --run_typer
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
18
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
19 #if $adv_param.unicycler_contigs:
1
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
20 --unicycler_contigs
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
21 #end if
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
22
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
23 #if $adv_param.run_overhang:
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
24 --run_overhang
1
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
25 #end if
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
26
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
27 #if $adv_param.debug:
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
28 --debug
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
29 #end if
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
30
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
31 #if $adv_param.plasmid_db
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
32 --plasmid_db '$adv_param.plasmid_db'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
33 #end if
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
34
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
35 #if $adv_param.plasmid_mash_db
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
36 --plasmid_mash_db '$adv_param.plasmid_mash_db'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
37 #end if
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
38
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
39 #if $adv_param.plasmid_meta
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
40 --plasmid_meta '$adv_param.plasmid_meta'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
41 #end if
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
42
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
43 #if $adv_param.repetitive_mask
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
44 --repetitive_mask '$adv_param.repetitive_mask'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
45 #end if
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
46
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
47 #if $adv_param.plasmid_mob
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
48 --plasmid_mob '$adv_param.plasmid_mob'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
49 #end if
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
50
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
51 #if $adv_param.plasmid_mpf
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
52 --plasmid_mpf '$adv_param.plasmid_mpf'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
53 #end if
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
54
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
55 #if $adv_param.plasmid_orit
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
56 --plasmid_orit '$adv_param.plasmid_orit'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
57 #end if
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
58
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
59 --min_length '${adv_param.min_length}'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
60 --min_rep_evalue '${adv_param.min_rep_evalue}'
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
61 --min_rep_evalue '${adv_param.min_rep_evalue}'
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
62 --min_mob_evalue '${adv_param.min_mob_evalue}'
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
63 --min_con_evalue '${adv_param.min_con_evalue}'
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
64 --min_rep_ident '${adv_param.min_rep_ident}'
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
65 --min_mob_ident '${adv_param.min_mob_ident}'
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
66 --min_con_ident '${adv_param.min_con_ident}'
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
67 --min_rpp_ident '${adv_param.min_rpp_ident}'
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
68
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
69 --min_rep_cov '${adv_param.min_rep_cov}'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
70 --min_mob_cov '${adv_param.min_mob_cov}'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
71 --min_con_cov '${adv_param.min_con_cov}'
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
72 --min_rpp_cov '${adv_param.min_rpp_cov}'
6
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
73 --outdir 'outdir' &&
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
74 mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true)
1
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
75 ]]>
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
76 </command>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
77 <inputs>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
78 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
79 <section name="adv_param" title="Advanced parameters" expanded="False">
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
80 <param name="unicycler_contigs" type="boolean" truevalue="true" falsevalue="" checked="true" label="Check for circularity flag generated by unicycler in contigs fasta headers?"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
81 <param name="run_overhang" type="boolean" truevalue="true" falsevalue="" checked="true" label="Detect circular contigs (i.e. potential plasmids) with assembly overhangs?"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
82 <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
83
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
84 <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001"/>
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
85 <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float" min="0.00001" max="1" value="0.00001"/>
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
86 <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float" min="0.00001" max="1" value="0.00001"/>
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
87 <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float" min="0.00001" max="1" value="0.00001"/>
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
88 <param name="min_length" label="Minimum length of contigs to classify" type="integer" value="1000"/>
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
89 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
90 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
91 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/>
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
92 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/>
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
93
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
94 <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
95 <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
96 <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"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
97 <param name="min_rpp_cov" label="Minimum percentage coverage of contigs by repetitive elements" type="integer" min="0" max="100" value="80"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
98
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
99 <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help=""/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
100 <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"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
101 <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help=""/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
102 <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help=""/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
103 <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help=""/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
104 <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help=""/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
105 <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help=""/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
106 <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help=""/>
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
107 </section>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
108 </inputs>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
109 <outputs>
6
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
110 <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/>
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
111 <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_results.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/>
6
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
112 <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: Chromosomal sequences"/>
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
113 <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: Plasmids">
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
114 <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" />
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
115 </collection>
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
116 </outputs>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
117 <tests>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
118 <test>
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
119 <param name="input" value="Ecoli_strain_KV7_complete_LT795502.fasta" ftype="fasta"/>
6
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
120 <section name="adv_param">
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
121 <param name="unicycler_contigs" value="True"/>
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
122 <param name="run_overhang" value="True"/>
6
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
123 </section>
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
124 <output name="contig_report">
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
125 <assert_contents>
7
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
126 <has_text text="chromosome"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
127 <has_text text="plasmid"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
128 <has_text text="IncHI1A"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
129 <has_text text="IncN"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
130 </assert_contents>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
131 </output>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
132 <output name="mobtyper_aggregate_report">
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
133 <assert_contents>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
134 <has_text text="conjugative"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
135 <has_text text="Gammaproteobacteria"/>
822575bf359f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
nml
parents: 6
diff changeset
136 <has_text text="223020"/>
6
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
137 </assert_contents>
9424de64bfa8 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
nml
parents: 5
diff changeset
138 </output>
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
139 </test>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
140 </tests>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
141 <help>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
142
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
143 **Syntax**
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
144
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
145 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
146
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
147 For more information please visit https://github.com/phac-nml/mob-suite/.
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
148
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
149 **Workflow**
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
150
4
1c5dfecfbb4d planemo upload for repository https://github.com/phac-nml/mob-suite commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents: 3
diff changeset
151 This preliminary \"Mobilome and Resistome Analysis Workflow\" linking mob_recon with staramr provides reports on mobilome and resistome for a given isolate given a draft genome assembly. The workflow is located in Shared Data --> Workflows --> Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR). The workflow file can also be manually downloaded from https://raw.githubusercontent.com/phac-nml/galaxy_tools/master/tools/mob_suite/workflows/AMRworkflow_STARAMR.ga.
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents: 1
diff changeset
152
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
153 -----
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
154
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
155 **Input:**
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
156
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
157 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
158
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
159
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
160 **Output:**
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
161
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
162 Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column.
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
163
1
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
164 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
165
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
166
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
167 </help>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
168 <citations>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
169 <citation type="bibtex">
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
170 @misc{githubmob-suite,
1
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
171 author = {Robertson J, Nash J},
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
172 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
173 publisher = {GitHub},
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
174 journal = {GitHub repository},
1
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
175 doi = {10.1099/mgen.0.000206},
2c419df5cdaa planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
nml
parents: 0
diff changeset
176 url = {https://github.com/phac-nml/mob-suite}
0
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
177 }</citation>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
178 </citations>
820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
nml
parents:
diff changeset
179 </tool>