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comparison mob_recon.xml @ 2:2c7f721a4905 draft

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planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
author nml
date Fri, 17 Aug 2018 11:12:08 -0400
parents 2c419df5cdaa
children 066b2a1c6a55
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1:2c419df5cdaa 2:2c7f721a4905
1 <tool id="mob_recon" name="MOB-Recon" version="1.4.5"> 1 <tool id="mob_recon" name="MOB-Recon" version="1.4.8">
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="1.4.5">mob_suite</requirement> 4 <requirement type="package" version="1.4.8">mob_suite</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
7 <![CDATA[ 7 <![CDATA[
8 ln -s "${input}" "${input.name}"; 8 #import re
9 #import os.path
9 10
10 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" 11 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta")
12 ln -s "$input" $named_input &&
13
14 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile "${named_input}"
11 #if str($adv_param.unicycler_contigs) == "True": 15 #if str($adv_param.unicycler_contigs) == "True":
12 --unicycler_contigs 16 --unicycler_contigs
13 #end if 17 #end if
14 #if str($adv_param.run_circlator) == "True": 18 #if str($adv_param.run_circlator) == "True":
15 --run_circlator 19 --run_circlator
16 #end if 20 #end if
17 #if str($adv_param.min_length_condition.min_length_param) == "True": 21 #if str($adv_param.min_length_condition.min_length_param) == "True":
18 --min_length ${adv_param.min_length_condition.min_length_value} 22 --min_length ${adv_param.min_length_condition.min_length_value}
19 #end if 23 #end if
20 --run_typer --outdir '.'; 24 --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}'
25 --min_rep_evalue '${adv_param.min_rep_evalue}'
26 --min_mob_evalue '${adv_param.min_mob_evalue}'
27 --min_con_evalue '${adv_param.min_con_evalue}'
28 --min_rep_ident '${adv_param.min_rep_ident}'
29 --min_mob_ident '${adv_param.min_mob_ident}'
30 --min_con_ident '${adv_param.min_con_ident}'
31 --min_rpp_ident '${adv_param.min_rpp_ident}'
32 --outdir '.' &&
33 mkdir ./sequences && (cp plasmid*.fasta chromosome.fasta ./sequences 2> /dev/null || true)
21 ]]> 34 ]]>
22 </command> 35 </command>
23 <inputs> 36 <inputs>
24 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> 37 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
25 <section name="adv_param" title="Advanced parameters" expanded="False"> 38 <section name="adv_param" title="Advanced parameters" expanded="False">
30 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True"> 43 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
31 <option value="True">Yes</option> 44 <option value="True">Yes</option>
32 <option value="False">No</option> 45 <option value="False">No</option>
33 </param> 46 </param>
34 <conditional name="min_length_condition"> 47 <conditional name="min_length_condition">
35 <param name="min_length_param" label="Minimum length of contigs to classify" type="select" value="False"> 48 <param name="min_length_param" label="Minimum length of contigs to process" type="select" value="False">
36 <option value="False">No</option> 49 <option value="False">No</option>
37 <option value="True">Yes</option> 50 <option value="True">Yes</option>
38 </param> 51 </param>
39 <when value="True"> 52 <when value="True">
40 <param name="min_length_value" type="integer" value="500" min="50"/> 53 <param name="min_length_value" type="integer" value="500" min="50"/>
41 </when> 54 </when>
42 <when value="False"/> 55 <when value="False"/>
43 </conditional> 56 </conditional>
57 <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001"/>
58 <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float" min="0.00001" max="1" value="0.00001"/>
59 <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float" min="0.00001" max="1" value="0.00001"/>
60 <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float" min="0.00001" max="1" value="0.00001"/>
61 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>
62 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>
63 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/>
64 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/>
44 </section> 65 </section>
45 </inputs> 66 </inputs>
46 <outputs> 67 <outputs>
47 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name}: Overall contig MOB-recon report"/> 68 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/>
48 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name}: Repetitive elements BLAST report"/> 69 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
49 <data name="outfile3" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name}: Chromosomal sequences"/> 70 <data name="outfile3" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
50 <data name="outfile4" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name}: Aggregate MOB-typer report for all contigs"/> 71 <collection name="seqhits" type="list" label="${tool.name} on ${on_string}: Extracted sequences (plasmids,chromosome(s))">
51 <data name="outfile5" format="fasta" label="${tool.name}: Plasmid sequence" hidden="true"> 72 <discover_datasets pattern="__name_and_ext__" directory="sequences" />
52 <discover_datasets pattern="plasmid_.+\.(?P&lt;ext&gt;.+)" ext="fasta" visible="true" assign_primary_output="false"/> 73 </collection>
53 </data>
54 </outputs> 74 </outputs>
55 <tests> 75 <tests>
56 <test> 76 <test>
57 <param name="input" value="plasmid_476.fasta" ftype="fasta"/> 77 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
58 <section name="adv_param"> 78 <section name="adv_param">
59 <param name="evalue" value="0.00001"/>
60 <param name="unicycler_contigs" value="True"/> 79 <param name="unicycler_contigs" value="True"/>
61 <param name="run_circlator" value="True"/> 80 <param name="run_circlator" value="True"/>
62 </section> 81 </section>
63 <output name="outfile1"> 82 <output name="outfile1">
64 <assert_contents> 83 <assert_contents>
72 **Syntax** 91 **Syntax**
73 92
74 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases. 93 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
75 94
76 For more information please visit https://github.com/phac-nml/mob-suite/. 95 For more information please visit https://github.com/phac-nml/mob-suite/.
96
97 **Workflow**
98
99 There is a preliminary Mobilome and Resistome Analysis Workflow linking mob_recon with staramr providing reports on mobilome and resistome https://github.com/phac-nml/mob-suite/.
77 100
78 ----- 101 -----
79 102
80 **Input:** 103 **Input:**
81 104