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annotate mob_recon.xml @ 4:1c5dfecfbb4d draft

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planemo upload for repository https://github.com/phac-nml/mob-suite commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
author nml
date Mon, 20 Aug 2018 16:03:51 -0400
parents 066b2a1c6a55
children 09424ec94e80
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1 <tool id="mob_recon" name="MOB-Recon" version="1.4.8">
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2 <description>Type contigs and extract plasmid sequences</description>
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3 <requirements>
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4 <requirement type="package" version="1.4.8">mob_suite</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 #import re
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9 #import os.path
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11 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta")
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12 ln -s "$input" $named_input &&
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14 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile "${named_input}"
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15 #if str($adv_param.unicycler_contigs) == "True":
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16 --unicycler_contigs
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17 #end if
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18 #if str($adv_param.run_circlator) == "True":
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19 --run_circlator
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20 #end if
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21 #if str($adv_param.min_length_condition.min_length_param) == "True":
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22 --min_length ${adv_param.min_length_condition.min_length_value}
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23 #end if
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24 --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}'
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25 --min_rep_evalue '${adv_param.min_rep_evalue}'
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26 --min_mob_evalue '${adv_param.min_mob_evalue}'
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27 --min_con_evalue '${adv_param.min_con_evalue}'
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28 --min_rep_ident '${adv_param.min_rep_ident}'
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29 --min_mob_ident '${adv_param.min_mob_ident}'
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30 --min_con_ident '${adv_param.min_con_ident}'
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31 --min_rpp_ident '${adv_param.min_rpp_ident}'
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32 --outdir '.' &&
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33 mkdir ./sequences && (cp plasmid*.fasta chromosome.fasta ./sequences 2> /dev/null || true)
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34 ]]>
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35 </command>
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36 <inputs>
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37 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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38 <section name="adv_param" title="Advanced parameters" expanded="False">
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39 <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">
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40 <option value="True">Yes</option>
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41 <option value="False">No</option>
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42 </param>
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43 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
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44 <option value="True">Yes</option>
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45 <option value="False">No</option>
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46 </param>
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47 <conditional name="min_length_condition">
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48 <param name="min_length_param" label="Minimum length of contigs to process" type="select" value="False">
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49 <option value="False">No</option>
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50 <option value="True">Yes</option>
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51 </param>
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52 <when value="True">
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53 <param name="min_length_value" type="integer" value="500" min="50"/>
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54 </when>
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55 <when value="False"/>
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56 </conditional>
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57 <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001"/>
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58 <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float" min="0.00001" max="1" value="0.00001"/>
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59 <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float" min="0.00001" max="1" value="0.00001"/>
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60 <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float" min="0.00001" max="1" value="0.00001"/>
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61 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>
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62 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>
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63 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/>
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64 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/>
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65 </section>
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66 </inputs>
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67 <outputs>
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68 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/>
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69 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
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70 <data name="outfile3" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
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71 <collection name="seqhits" type="list" label="${tool.name} on ${on_string}: Extracted sequences (plasmids,chromosome(s))">
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72 <discover_datasets pattern="__name_and_ext__" directory="sequences" />
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73 </collection>
0
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
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78 <section name="adv_param">
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79 <param name="unicycler_contigs" value="True"/>
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80 <param name="run_circlator" value="True"/>
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81 </section>
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82 <output name="outfile1">
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83 <assert_contents>
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84 <has_text text="NC_019097"/>
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85 </assert_contents>
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86 </output>
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87 </test>
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88 </tests>
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89 <help>
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90
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91 **Syntax**
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92
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93 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
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94
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95 For more information please visit https://github.com/phac-nml/mob-suite/.
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96
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97 **Workflow**
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98
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99 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.
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100
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101 -----
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102
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103 **Input:**
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104
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105 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
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106
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107
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108 **Output:**
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109
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110 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.
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111
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112 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
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113
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114
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115 </help>
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116 <citations>
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117 <citation type="bibtex">
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118 @misc{githubmob-suite,
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119 author = {Robertson J, Nash J},
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120 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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121 publisher = {GitHub},
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122 journal = {GitHub repository},
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123 doi = {10.1099/mgen.0.000206},
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124 url = {https://github.com/phac-nml/mob-suite}
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125 }</citation>
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126 </citations>
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127 </tool>