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annotate mob_typer.xml @ 1:2c419df5cdaa draft

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planemo upload for repository https://github.com/phac-nml/mob-suite commit 7681cd156a24e77ca039f3137145b6949a2ad5a3
author nml
date Thu, 26 Jul 2018 14:50:59 -0400
parents 820eec3fa31f
children 2c7f721a4905
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1 <tool id="mob_typer" name="MOB-Typer" version="1.4.5">
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="1.4.5">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[
0
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8 ln -s "${input}" "${input.name}";
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9 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}"
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10 #if str($adv_param.min_rep_evalue_condition.min_rep_evalue_param) == "True":
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11 --min_rep_evalue $adv_param.min_rep_evalue_condition.min_rep_evalue_value
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12 #end if
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13 #if str($adv_param.min_mob_evalue_condition.min_mob_evalue_param) == "True":
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14 --min_mob_evalue $adv_param.min_mob_evalue_condition.min_mob_evalue_value
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15 #end if
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16 #if str($adv_param.min_con_evalue_condition.min_con_evalue_param) == "True":
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17 --min_con_evalue $adv_param.min_con_evalue_condition.min_con_evalue_value
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18 #end if
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19 #if str($adv_param.min_ori_evalue_condition.min_ori_evalue_param) == "True":
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20 --min_ori_evalue $adv_param.min_ori_evalue_condition.min_ori_evalue_value
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21 #end if
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22 --outdir '.';
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23 ]]>
0
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24 </command>
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25 <inputs>
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26 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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27 <section name="adv_param" title="Advanced parameters" expanded="False">
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28 <conditional name="min_rep_evalue_condition">
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29 <param name="min_rep_evalue_param" label="Minimum evalue threshold for replicon blastn" type="select" value="False">
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30 <option value="False">No</option>
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31 <option value="True">Yes</option>
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32 </param>
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33 <when value="True">
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34 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/>
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35 </when>
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36 <when value="False"/>
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37 </conditional>
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38 <conditional name="min_mob_evalue_condition">
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39 <param name="min_mob_evalue_param" label="Minimum evalue threshold for relaxase tblastn" type="select" value="False">
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40 <option value="False">No</option>
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41 <option value="True">Yes</option>
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42 </param>
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43 <when value="True">
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44 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="e-value (default: 0.00001)"/>
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45 </when>
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46 <when value="False"/>
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47 </conditional>
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48 <conditional name="min_con_evalue_condition">
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49 <param name="min_con_evalue_param" label="Minimum evalue threshold for contig blastn" type="select" value="False">
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50 <option value="False">No</option>
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51 <option value="True">Yes</option>
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52 </param>
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53 <when value="True">
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54 <param name="min_con_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/>
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55 </when>
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56 <when value="False"/>
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57 </conditional>
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58 <conditional name="min_ori_evalue_condition">
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59 <param name="min_ori_evalue_param" label="Minimum evalue threshold for oriT elements blastn" type="select" value="False">
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60 <option value="False">No</option>
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61 <option value="True">Yes</option>
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62 </param>
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63 <when value="True">
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64 <param name="min_ori_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/>
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65 </when>
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66 <when value="False"/>
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67 </conditional>
0
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68 </section>
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69 </inputs>
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70 <outputs>
1
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71 <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
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72 <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
0
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73 </data>
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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 <assert_stdout>
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79 <has_text text="JN253636"/>
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80 </assert_stdout>
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81 </test>
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82 </tests>
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83 <help>
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84
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85 **Syntax**
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86
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87 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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88
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89 For more information please visit https://github.com/phac-nml/mob-suite/.
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90
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91 -----
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92
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93 **Input:**
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94
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95 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
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96
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97
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98 **Output:**
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99
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100 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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101
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102
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103 </help>
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104 <citations>
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105 <citation type="bibtex">
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106 @misc{githubmob-suite,
1
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107 author = {Robertson J, Nash J},
0
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108 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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109 publisher = {GitHub},
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110 journal = {GitHub repository},
1
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111 doi = {10.1099/mgen.0.000206},
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112 url = {https://github.com/phac-nml/mob-suite}
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113 }</citation>
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114 </citations>
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115 </tool>