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annotate abritamr.xml @ 5:468fd92deaaa draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit 1550e33e5b13d9e8761c362e47fc473721a13d5a
author iuc
date Sat, 19 Oct 2024 20:56:13 +0000
parents e909d3bc4687
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6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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1 <tool id="abritamr" name="abriTAMR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>AMR gene detection with AMRFinderPlus</description>
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3 <macros>
4
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4 <token name="@TOOL_VERSION@">1.0.19</token>
5
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5 <token name="@VERSION_SUFFIX@">1</token>
0
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6 <token name="@PROFILE@">22.05</token>
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7 </macros>
3
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8 <xrefs>
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9 <xref type="bio.tools">abritamr</xref>
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10 </xrefs>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">abritamr</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code"><![CDATA[
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15 abritamr run
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16 --contigs '$input_tsv'
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17 #if $species:
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18 --species '$species'
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19 #end if
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20 #if $identity:
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21 --identity '$identity'
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22 #end if
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23 --jobs \${GALAXY_SLOTS:-4}
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24 ]]></command>
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25 <configfiles>
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26 <configfile name="input_tsv">
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27 #for $i in $contig:
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28 ${i.element_identifier} ${i}
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29 #end for
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30 </configfile>
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31 </configfiles>
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32 <inputs>
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33 <param name="contig" type="data" format="fasta" multiple="true" label="Input contigs"/>
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34 <param argument="species" type="select" multiple="false" optional="true" label="Specify species to aquire resistance mechanisms as point mutations">
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35 <option value="Neisseria">Neisseria</option>
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36 <option value="Clostridioides_difficile">Clostridioides difficile</option>
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37 <option value="Acinetobacter_baumannii">Acinetobacter baumannii</option>
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38 <option value="Campylobacter">Campylobacter</option>
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39 <option value="Enterococcus_faecalis">Enterococcus faecalis</option>
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40 <option value="Enterococcus_faecium">Enterococcus faecium</option>
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41 <option value="Escherichia">Escherichia</option>
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42 <option value="Klebsiella">Klebsiella</option>
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43 <option value="Salmonella">Salmonella</option>
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44 <option value="Staphylococcus_aureus">Staphylococcus aureus</option>
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45 <option value="Staphylococcus_pseudintermedius">Staphylococcus pseudintermedius</option>
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46 <option value="Streptococcus_agalactiae">Streptococcus agalactiae</option>
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47 <option value="Streptococcus_pneumoniae">Streptococcus pneumoniae</option>
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48 <option value="Streptococcus_pyogenes">Streptococcus pyogenes</option>
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49 </param>
1
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50 <param argument="identity" type="float" optional="true" min="0.0" max="1.0" label="Minimum identity of matches with armfinder" help="The default is unset, uses a curated threshold for the gene if present, otherwise defaults to 0.9."/>
0
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51 <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/>
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52 </inputs>
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53 <outputs>
5
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54 <data name="abriTAMR_output" format="tabular" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" />
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55 <data name="matches_summary" format="tabular" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/>
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56 <data name="partials_summary" format="tabular" label="${tool.name} on ${on_string}: partials summary" from_work_dir="summary_partials.txt"/>
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57 <data name="virulence_summary" format="tabular" label="${tool.name} on ${on_string}: virulence summary" from_work_dir="summary_virulence.txt"/>
0
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58 <data name="log" format="txt" label="${tool.name} on ${on_string}: log file" from_work_dir="abritamr.log">
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59 <filter>log_file</filter>
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60 </data>
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61 </outputs>
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62 <tests>
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63 <!-- Single sample, with logfile -->
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64 <test expect_num_outputs="5">
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65 <param name="contig" value="CP009102.1.fasta" />
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66 <param name="log_file" value="true" />
5
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67 <output name="virulence_summary" ftype="tabular">
0
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68 <assert_contents>
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69 <has_n_lines n="2"/>
2
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70 <has_text text="sinH"/>
5
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71 <has_n_columns n="2"/>
0
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72 </assert_contents>
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73 </output>
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74 </test>
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75 <!-- Multiple samples, no logfile -->
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76 <test expect_num_outputs="4">
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77 <param name="contig" value="NC_003198.1_1kb.fasta,NC_011750.1_1kb.fasta" />
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78 <param name="species" value="Salmonella" />
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79 <param name="identity" value="0.9" />
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80 <param name="log_file" value="false" />
5
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81 <output name="virulence_summary" ftype="tabular">
0
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82 <assert_contents>
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83 <has_n_lines n="3"/>
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84 <has_text text="NC_003198.1_1kb.fasta"/>
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85 <has_n_columns n="1"/>
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86 </assert_contents>
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87 </output>
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88 </test>
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89 </tests>
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90 <help>
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91 *Taming the AMR beast*
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92
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93 abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia.
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94 + Acquired resistance mechanims in the form of point mutations (restricted to subset of species)
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95 + Streamlined output.
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96 + Presence of virulence factors
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97 </help>
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98 <citations>
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99 <citation type="doi">10.5281/zenodo.7370627</citation>
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100 </citations>
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101 </tool>