Mercurial > repos > dfornika > mob_recon

annotate mob_recon.xml @ 3:84cf5ed52f58 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/phac-nml/mob-suite commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Tue, 05 Nov 2019 17:17:47 -0500
parents 98a686bf8d1c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
b926a710e788 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 0
diff changeset
1 <tool id="mob_recon" name="MOB-Recon" version="2.0.1_galaxy0">
0
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
2 <description>Type contigs and extract plasmid sequences</description>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
3 <requirements>
1
b926a710e788 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 0
diff changeset
4 <requirement type="package" version="2.0.1">mob_suite</requirement>
0
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
5 </requirements>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
6 <command detect_errors="exit_code">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
7 <![CDATA[
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
8 #import re
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
9 #import os.path
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
10
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
11 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta")
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
12 ln -s "$input" $named_input &&
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
13
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
14 mob_recon
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
15 --num_threads \${GALAXY_SLOTS:-4}
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
16 --infile "${named_input}"
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
17 #if str($adv_param.unicycler_contigs) == "True":
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
18 --unicycler_contigs
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
19 #end if
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
20 #if str($adv_param.run_circlator) == "True":
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
21 --run_circlator
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
22 #end if
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
23 #if str($adv_param.min_length_condition.min_length_param) == "True":
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
24 --min_length ${adv_param.min_length_condition.min_length_value}
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
25 #end if
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
26 --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}'
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
27 --min_rep_evalue '${adv_param.min_rep_evalue}'
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
28 --min_mob_evalue '${adv_param.min_mob_evalue}'
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
29 --min_con_evalue '${adv_param.min_con_evalue}'
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
30 --min_rep_ident '${adv_param.min_rep_ident}'
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
31 --min_mob_ident '${adv_param.min_mob_ident}'
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
32 --min_con_ident '${adv_param.min_con_ident}'
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
33 --min_rpp_ident '${adv_param.min_rpp_ident}'
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
34 --outdir '.' &&
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
35 mkdir ./plasmids &&
2
98a686bf8d1c "planemo upload for repository https://github.com/phac-nml/mob-suite commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 1
diff changeset
36 (cp plasmid*.fasta ./plasmids 2> /dev/null || true)
0
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
37 ]]>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
38 </command>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
39 <inputs>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
40 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
41 <section name="adv_param" title="Advanced parameters" expanded="False">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
42 <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
43 <option value="True">Yes</option>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
44 <option value="False">No</option>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
45 </param>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
46 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
47 <option value="True">Yes</option>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
48 <option value="False">No</option>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
49 </param>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
50 <conditional name="min_length_condition">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
51 <param name="min_length_param" label="Minimum length of contigs to process" type="select" value="False">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
52 <option value="False">No</option>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
53 <option value="True">Yes</option>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
54 </param>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
55 <when value="True">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
56 <param name="min_length_value" type="integer" value="500" min="50"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
57 </when>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
58 <when value="False"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
59 </conditional>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
60 <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
61 <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float" min="0.00001" max="1" value="0.00001"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
62 <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float" min="0.00001" max="1" value="0.00001"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
63 <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float" min="0.00001" max="1" value="0.00001"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
64 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
65 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
66 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
67 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
68 </section>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
69 </inputs>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
70 <outputs>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
71 <data name="contig_report" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
72 <data name="repetitive_blast_report" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
3
84cf5ed52f58 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 2
diff changeset
73 <data name="chromosome" type="data" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name} on ${on_string}: Chromosome"/>
84cf5ed52f58 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 2
diff changeset
74 <collection name="plasmids" type="list" label="${tool.name} on ${on_string}: Plasmids">
84cf5ed52f58 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 2
diff changeset
75 <discover_datasets pattern="__name_and_ext__" directory="plasmids" />
84cf5ed52f58 "planemo upload for repository https://github.com/phac-nml/mob-suite commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 2
diff changeset
76 </collection>
0
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
77 </outputs>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
78 <tests>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
79 <test>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
80 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
81 <section name="adv_param">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
82 <param name="unicycler_contigs" value="True"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
83 <param name="run_circlator" value="True"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
84 </section>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
85 <output name="outfile1">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
86 <assert_contents>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
87 <has_text text="NC_019097"/>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
88 </assert_contents>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
89 </output>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
90 </test>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
91 </tests>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
92 <help>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
93 **Syntax**
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
94
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
95 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
96
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
97 For more information please visit https://github.com/phac-nml/mob-suite/.
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
98
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
99 **Workflow**
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
100
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
101 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.
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
102
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
103 -----
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
104
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
105 **Input:**
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
106
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
107 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
108
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
109
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
110 **Output:**
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
111
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
112 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.
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
113
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
114 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
115 </help>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
116 <citations>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
117 <citation type="bibtex">
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
118 @misc{githubmob-suite,
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
119 author = {Robertson J, Nash J},
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
120 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
121 publisher = {GitHub},
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
122 journal = {GitHub repository},
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
123 doi = {10.1099/mgen.0.000206},
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
124 url = {https://github.com/phac-nml/mob-suite}
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
125 }
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
126 </citation>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
127 </citations>
d793a3479e7f "planemo upload for repository https://github.com/phac-nml/mob-suite commit 62e7cd82cb9b209bf3f797ae288916e88bbe8bc6-dirty"
dfornika
parents:
diff changeset
128 </tool>