Mercurial > repos > dfornika > mob_suite

annotate mob_hostrange.xml @ 43:21ccebc96bd9 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit d5db17429118cd74a85986c49b917caec6f952bd-dirty"
author dfornika
date Thu, 14 Nov 2019 01:19:58 +0000
parents cd69d25ce451
children e2b09f608636
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1 <tool id="mob_hostrange" name="MOB-Hostrange" version="2.0.2+galaxy0">
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2 <description>
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3 Provides information on plasmid reproductive host range and transfer rate using both sequencing
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4 and experimental data from public databases (NCBI) and publications (PubMED).
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5 </description>
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6 <requirements>
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7 <requirement type="package" version="2.0.2">mob_suite</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 mob_hostrange
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12 ${exact_match}
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13 ${loose_match}
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14 ${host_range_detailed}
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15 #if str(${replicon_name}) != "":
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16 --replicon_name '${replicon_name}'
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17 #end if
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18 #if str(${relaxase_name}) != "":
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19 --relaxase_name '${relaxase_name}'
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20 #end if
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21 #if str(${relaxase_accession}) != "":
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22 --relaxase_accession '${relaxase_accession}'
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23 #end if
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24 #if str(${cluster_id}) != "":
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25 --cluster_id '${cluster_id}'
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26 #end if
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27 --inputseq "${inputseq}"
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28 --outdir '.'
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param name="inputseq" type="data" format="fasta" label="Input" help="plasmid FASTA file"/>
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33 <param name="exact_match" type="boolean" truevalue="--exact_match" falsevalue="" checked="false"/>
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34 <param name="loose_match" type="boolean" truevalue="--loose_match" falsevalue="" checked="false"/>
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35 <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="false"/>
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36 <param name="replicon_name" type="text" />
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37 <param name="relaxase_name" type="text" />
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38 <param name="relaxase_accession" type="text" />
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39 <param name="cluster_id" type="text" />
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40 </inputs>
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41 <outputs>
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42 <data name="hostrange_phylostats" label="${tool.name}: Phylostats report on ${input.name}" format="tabular">
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43 <discover_datasets pattern=".+hostrange_phylostats\.txt" visible="true" format="tabular" />
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44 </data>
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45 <data name="hostrange_report" label="${tool.name}: Hostrange report on ${input.name}" format="tabular">
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46 <discover_datasets pattern=".+hostrange_report\.txt" visible="true" format="tabular" />
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47 </data>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="inputseq" value="plasmid_476.fasta" ftype="fasta"/>
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52 <assert_stderr>
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53 <has_text text="RefSeq Plasmid database found no hits"/>
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54 </assert_stderr>
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55 </test>
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56 </tests>
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57 <help>
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58
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59 **Syntax**
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60
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61 This tool provides information on plasmid reproductive host range and transfer rate using both sequencing and experimental data from public databases (NCBI) and publications (PubMED). The predicted host range represents a range of putative hosts where a given plasmid can stably replicate and be maintained by the host. The host range module makes no source attribution predictions of a plasmid.
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62
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63 For more information please visit https://github.com/phac-nml/mob-suite/.
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64
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65 -----
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66
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67 **Input:**
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68
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69 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
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70
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71
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72 **Output:**
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73
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74 Tab-delimited reports listing predicted hostrange information. Refer to https://github.com/phac-nml/mob-suite#mob-hostrange-report-file-format for the description of each column.
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75
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76
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77 </help>
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78 <citations>
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79 <citation type="bibtex">
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80 @misc{githubmob-suite,
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81 author = {Robertson J, Nash J},
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82 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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83 publisher = {GitHub},
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84 journal = {GitHub repository},
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85 doi = {10.1099/mgen.0.000206},
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86 url = {https://github.com/phac-nml/mob-suite}
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87 }</citation>
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88 </citations>
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89 </tool>