Mercurial > repos > nml > mob_suite

annotate mob_recon.xml @ 10:2fd93022d5d7 draft default tip

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite commit 8bd2d0ff4101e7e7e6a45247d616929593a03cd4
author nml
date Fri, 21 Feb 2025 18:41:14 +0000
parents 53f50adcb78e
children
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1 <tool id="mob_recon" name="MOB-Recon" version="@VERSION@+galaxy0">
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2 <description>Type contigs and extract plasmid sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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8 <version_command>mob_recon --version</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 #import re
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12 #import os.path
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14 #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta')
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15 ln -s '$input' '$named_input' &&
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18 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile '${named_input}'
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20 #if $adv_param.unicycler_contigs:
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21 --unicycler_contigs
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22 #end if
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24 #if $adv_param.run_overhang:
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25 --run_overhang
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26 #end if
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28 #if $adv_param.debug:
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29 --debug
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30 #end if
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32 #if $adv_param.plasmid_db
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33 --plasmid_db '$adv_param.plasmid_db'
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34 #end if
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36 #if $adv_param.plasmid_mash_db
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37 --plasmid_mash_db '$adv_param.plasmid_mash_db'
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38 #end if
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40 #if $adv_param.plasmid_meta
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41 --plasmid_meta '$adv_param.plasmid_meta'
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42 #end if
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44 #if $adv_param.repetitive_mask
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45 --repetitive_mask '$adv_param.repetitive_mask'
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46 #end if
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48 #if $adv_param.plasmid_mob
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49 --plasmid_mob '$adv_param.plasmid_mob'
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50 #end if
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52 #if $adv_param.plasmid_mpf
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53 --plasmid_mpf '$adv_param.plasmid_mpf'
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54 #end if
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56 #if $adv_param.plasmid_orit
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57 --plasmid_orit '$adv_param.plasmid_orit'
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58 #end if
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59
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60 #if $adv_param.filter_db
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61 --filter_db '$adv_param.filter_db'
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62 #end if
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64 --mash_genome_neighbor_threshold '${adv_param.mash_genome_neighbor_threshold}'
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65 --primary_cluster_dist '${adv_param.primary_cluster_dist}'
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66 --secondary_cluster_dist '${adv_param.secondary_cluster_dist}'
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67 --max_contig_size '${adv_param.max_contig_size}'
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68 --max_plasmid_size '${adv_param.max_plasmid_size}'
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69
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70 --min_length '${adv_param.min_length}'
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71 --min_rep_evalue '${adv_param.min_rep_evalue}'
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72 --min_rep_evalue '${adv_param.min_rep_evalue}'
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73 --min_mob_evalue '${adv_param.min_mob_evalue}'
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74 --min_con_evalue '${adv_param.min_con_evalue}'
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75 --min_rep_ident '${adv_param.min_rep_ident}'
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76 --min_mob_ident '${adv_param.min_mob_ident}'
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77 --min_con_ident '${adv_param.min_con_ident}'
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78 --min_rpp_ident '${adv_param.min_rpp_ident}'
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80 --min_rep_cov '${adv_param.min_rep_cov}'
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81 --min_mob_cov '${adv_param.min_mob_cov}'
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82 --min_con_cov '${adv_param.min_con_cov}'
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83 --min_rpp_cov '${adv_param.min_rpp_cov}'
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85
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86 --outdir 'outdir' &&
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87 mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true)
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88 ]]>
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89 </command>
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90 <inputs>
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91 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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92 <section name="adv_param" title="Advanced parameters" expanded="False">
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93
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94 <param name="unicycler_contigs" type="boolean" truevalue="true" falsevalue="" checked="true" label="Check for circularity flag generated by unicycler in contigs fasta headers?" help="(--unicycler_contigs)"/>
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95 <param name="run_overhang" type="boolean" truevalue="true" falsevalue="" checked="true" label="Detect circular contigs (i.e. potential plasmids) with assembly overhangs?" help="(--run_overhang)"/>
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96 <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" help="(--debug)"/>
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97 <param name="mash_genome_neighbor_threshold" label="Mash distance selecting valid closed genomes to filter" type="float" min="0.00001" max="1" value="0.002" help="(--mash_genome_neighbor_threshold)"/>
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98 <param name="primary_cluster_dist" label="MASH distance for assigning primary plasmid cluster id" type="float" min="0.00001" max="1" value="0.06" help="(--primary_cluster_dist)"/>
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99 <param name="secondary_cluster_dist" label="MASH distance for assigning secondary plasmid cluster id" type="float" min="0.00001" max="1" value="0.025" help="(--secondary_cluster_dist)"/>
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100 <param name="max_contig_size" label="Maximum size of a contig to be considered a plasmid (bp)" type="integer" min="1" max="1000000" value="450000" help="(--max_contig_size)"/>
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101 <param name="max_plasmid_size" label="Maximum size of a reconstructed plasmid (bp)" type="integer" min="1" max="1000000" value="450000" help="(--max_plasmid_size)"/>
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102
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103 <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001" help="(--min_rep_evalue)"/>
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104 <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float" min="0.00001" max="1" value="0.00001" help="(--min_mob_evalue)"/>
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105 <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float" min="0.00001" max="1" value="0.00001" help="(--min_con_evalue)"/>
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106 <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float" min="0.00001" max="1" value="0.00001" help="(--min_rpp_evalue)"/>
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107 <param name="min_length" label="Minimum length of contigs to classify (bp)" type="integer" value="1000" help="(--min_length)"/>
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108 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80" help="(--min_rep_ident)"/>
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109 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80" help="(--min_mob_ident)"/>
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110 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80" help="(--min_con_ident)"/>
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111 <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80" help="(--min_rpp_ident)"/>
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112
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113 <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80" help="(--min_rep_cov)"/>
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114 <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80" help="(--min_mob_cov)"/>
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115 <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" help="(--min_con_cov)"/>
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116 <param name="min_rpp_cov" label="Minimum percentage coverage of contigs by repetitive elements" type="integer" min="0" max="100" value="80" help="(--min_rpp_cov)"/>
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117
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118 <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference custom database of complete plasmids" help="(--plasmid_db)"/>
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119 <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 (--plasmid_mash_db)"/>
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120 <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="(--plasmid_meta)"/>
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121 <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="(--plasmid_replicons)"/>
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122 <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="(--reptitive_mask)"/>
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123 <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="(--plasmid_mob)"/>
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124 <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="(--plasmid_mpf)"/>
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125 <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="(--plasmid_orit)"/>
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126 <param name="filter_db" type="data" optional="true" format="fasta" label="Path to fasta file to mask sequences" help="(--filter_db)"/>
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127
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128
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129
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130 </section>
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131 </inputs>
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132 <outputs>
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133 <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/>
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134 <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_results.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/>
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135 <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: CHROMOSOMAL contigs"/>
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136 <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: PLASMIDS RECONSTRUCTED">
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137 <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" />
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138 </collection>
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139 </outputs>
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140 <tests>
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141 <test>
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142 <param name="input" value="Ecoli_strain_KV7_complete_LT795502.fasta" ftype="fasta"/>
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143 <section name="adv_param">
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144 <param name="unicycler_contigs" value="True"/>
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145 <param name="run_overhang" value="True"/>
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146 </section>
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147 <output name="contig_report">
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148 <assert_contents>
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149 <has_text text="chromosome"/>
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150 <has_text text="plasmid"/>
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151 <has_text text="IncHI1A"/>
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152 <has_text text="IncN"/>
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153 </assert_contents>
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154 </output>
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155 <output name="mobtyper_aggregate_report">
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156 <assert_contents>
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157 <has_text text="conjugative"/>
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158 <has_text text="Gammaproteobacteria"/>
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159 <has_text text="223020"/>
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160 </assert_contents>
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161 </output>
0
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162 </test>
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163 </tests>
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164 <help>
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165
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166 **Syntax**
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167
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168 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
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169
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170 For more information please visit https://github.com/phac-nml/mob-suite/.
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171
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172 -----
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173
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174 **Input:**
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175
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176 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
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177
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178
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179 **Output:**
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180
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181 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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182
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183 **Note:** Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
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184
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185
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186 </help>
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187 <citations>
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188 <citation type="bibtex">
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189 @misc{githubmob-suite,
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190 author = {Robertson J, Nash J},
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191 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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192 publisher = {GitHub},
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193 journal = {GitHub repository},
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194 doi = {10.1099/mgen.0.000206},
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195 url = {https://github.com/phac-nml/mob-suite}
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196 }</citation>
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197 </citations>
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198 </tool>