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annotate mob_typer.xml @ 7:822575bf359f draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b"
author nml
date Fri, 05 Jun 2020 13:02:15 -0400
parents 9424de64bfa8
children 53f50adcb78e
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1 <tool id="mob_typer" name="MOB-Typer" version="3.0.0">
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2 <description>Get the plasmid type and mobility given its sequence</description>
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3 <requirements>
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4 <requirement type="package" version="3.0.0">mob_suite</requirement>
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5 </requirements>
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6 <version_command>mob_typer --version</version_command>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 ln -s '${input}' '${input.name}' &&
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10 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile '${input.name}'
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13 #if $adv_param.multi
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14 --multi
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15 #end if
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17 --min_rep_evalue '$adv_param.min_rep_evalue_value'
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18 --min_mob_evalue '$adv_param.min_mob_evalue_value'
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19 --min_con_evalue '$adv_param.min_con_evalue_value'
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20 --min_length '$adv_param.min_length'
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21 --min_rep_ident '$adv_param.min_rep_ident'
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22 --min_mob_ident '$adv_param.min_mob_ident'
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24 --min_con_ident '$adv_param.min_con_ident'
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25 --min_rep_cov '$adv_param.min_rep_cov'
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26 --min_mob_cov '$adv_param.min_mob_cov'
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27 --min_con_cov '$adv_param.min_con_cov'
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28 --min_overlap '$adv_param.min_overlap'
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30 #if $adv_param.plasmid_db
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31 --plasmid_db '$adv_param.plasmid_db'
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32 #end if
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35 #if $adv_param.plasmid_mash_db
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36 --plasmid_mash_db '$adv_param.plasmid_mash_db'
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37 #end if
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39 #if $adv_param.plasmid_meta
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40 --plasmid_meta '$adv_param.plasmid_meta'
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41 #end if
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43 #if $adv_param.repetitive_mask
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44 --repetitive_mask '$adv_param.repetitive_mask'
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45 #end if
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47 #if $adv_param.plasmid_mob
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48 --plasmid_mob '$adv_param.plasmid_mob'
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49 #end if
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51 #if $adv_param.plasmid_mpf
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52 --plasmid_mpf '$adv_param.plasmid_mpf'
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53 #end if
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55 #if $adv_param.plasmid_orit
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56 --plasmid_orit '$adv_param.plasmid_orit'
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57 #end if
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59 #if $adv_param.debug
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60 --debug
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61 #end if
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63 --out_file plasmid_report.txt;
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65 ]]>
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66 </command>
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67 <inputs>
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68 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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69 <section name="adv_param" title="Advanced parameters" expanded="False">
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70 <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independant plasmid?" />
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71 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/>
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72 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/>
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73 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/>
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74 <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify"/>
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75 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>
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76 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>
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77 <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/>
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78 <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80"/>
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79 <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80"/>
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80 <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="70"/>
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81 <param name="min_overlap" label="Minimum overlap of fragments" type="integer" min="0" max="100" value="10"/>
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82 <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" />
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83 <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help=""/>
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84 <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="Companion MASH database of reference database"/>
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85 <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="MOB-cluster plasmid cluster formatted metadata file matched to the reference plasmid db"/>
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86 <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="FASTA of plasmid replicons"/>
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87 <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="FASTA of known repetitive elements"/>
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88 <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="FASTA of plasmid relaxases"/>
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89 <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="FASTA of known plasmid mate-pair proteins"/>
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90 <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT dna sequences"/>
6
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91 </section>
0
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92 </inputs>
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93 <outputs>
7
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94 <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" />
0
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95 </outputs>
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96 <tests>
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97 <test>
7
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98 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
6
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99 <output name="plasmid_report">
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100 <assert_contents>
7
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101 <has_text text="KJ484639"/>
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102 <has_text text="MOBP"/>
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103 <has_text text="NC_019097"/>
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104 <has_text text="conjugative"/>
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105 <has_text text="AA474"/>
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106 <has_text text="AI614"/>
6
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107 <has_text_matching expression="family\tEnterobacteriaceae"/>
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108 </assert_contents>
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109 </output>
0
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110 </test>
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111 </tests>
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112 <help>
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113
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114 **Syntax**
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115
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116 This tool provides *in-silico* predictions on plasmid typing including identification of replicon, relaxase and mate-pair formation protein types. MOB-typer also predicts mobility of a plasmid (Conjugative, Mobilizable, Non-mobilizable). Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single plasmid.
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117
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118 For more information please visit https://github.com/phac-nml/mob-suite/.
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119
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120 -----
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121
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122 **Input:**
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123
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124 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
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125
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126
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127 **Output:**
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128
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129 Tab-delimited report listing identified plasmid(s) and their predicted mobility. Refer to https://github.com/phac-nml/mob-suite#mob-typer-report-file-format for the description of each column.
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130
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131
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132 </help>
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133 <citations>
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134 <citation type="bibtex">
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135 @misc{githubmob-suite,
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136 author = {Robertson J, Nash J},
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137 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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138 publisher = {GitHub},
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139 journal = {GitHub repository},
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140 doi = {10.1099/mgen.0.000206},
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141 url = {https://github.com/phac-nml/mob-suite}
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142 }</citation>
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143 </citations>
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144 </tool>