Mercurial > repos > iuc > abritamr

annotate abritamr.xml @ 0:6085c9fbda49 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
author iuc
date Tue, 09 May 2023 11:09:18 +0000
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children f564aae1b543
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6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
iuc
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1 <tool id="abritamr" name="abriTAMR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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2 <description>AMR gene detection with AMRFinderPlus</description>
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.14</token>
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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5 <token name="@VERSION_SUFFIX@">0</token>
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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6 <token name="@PROFILE@">22.05</token>
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">abritamr</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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12 abritamr run
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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13 --contigs '$input_tsv'
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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14 #if $species:
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15 --species '$species'
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16 #end if
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17 #if $identity:
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18 --identity '$identity'
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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19 #end if
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20 --jobs \${GALAXY_SLOTS:-4}
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21 ]]></command>
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22 <configfiles>
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23 <configfile name="input_tsv">
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24 #for $i in $contig:
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25 ${i.element_identifier} ${i}
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26 #end for
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27 </configfile>
6085c9fbda49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit a5681252a5c94a4518ec8253f1cc3a3e4c8dba44
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28 </configfiles>
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29 <inputs>
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30 <param name="contig" type="data" format="fasta" multiple="true" label="Input contigs"/>
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31 <param argument="species" type="select" multiple="false" optional="true" label="Specify species to aquire resistance mechanisms as point mutations">
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32 <option value="Neisseria">Neisseria</option>
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33 <option value="Clostridioides_difficile">Clostridioides difficile</option>
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34 <option value="Acinetobacter_baumannii">Acinetobacter baumannii</option>
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35 <option value="Campylobacter">Campylobacter</option>
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36 <option value="Enterococcus_faecalis">Enterococcus faecalis</option>
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37 <option value="Enterococcus_faecium">Enterococcus faecium</option>
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38 <option value="Escherichia">Escherichia</option>
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39 <option value="Klebsiella">Klebsiella</option>
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40 <option value="Salmonella">Salmonella</option>
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41 <option value="Staphylococcus_aureus">Staphylococcus aureus</option>
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42 <option value="Staphylococcus_pseudintermedius">Staphylococcus pseudintermedius</option>
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43 <option value="Streptococcus_agalactiae">Streptococcus agalactiae</option>
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44 <option value="Streptococcus_pneumoniae">Streptococcus pneumoniae</option>
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45 <option value="Streptococcus_pyogenes">Streptococcus pyogenes</option>
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46 </param>
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47 <param argument="identity" value="0.9" type="float" optional="true" min="0.0" max="1" label="Minimum identity of matches with armfinder. Default: 0.9, unless curated threshold is present for the gene."/>
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48 <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/>
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49 </inputs>
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50 <outputs>
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51 <data name="abriTAMR_output" format="txt" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" />
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52 <data name="matches_summary" format="txt" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/>
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53 <data name="partials_summary" format="txt" label="${tool.name} on ${on_string}: partials summary" from_work_dir="summary_partials.txt"/>
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54 <data name="virulence_summary" format="txt" label="${tool.name} on ${on_string}: virulence summary" from_work_dir="summary_virulence.txt"/>
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55 <data name="log" format="txt" label="${tool.name} on ${on_string}: log file" from_work_dir="abritamr.log">
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56 <filter>log_file</filter>
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57 </data>
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58 </outputs>
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59 <tests>
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60 <!-- Single sample, with logfile -->
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61 <test expect_num_outputs="5">
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62 <param name="contig" value="CP009102.1.fasta" />
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63 <param name="log_file" value="true" />
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64 <output name="virulence_summary" ftype="txt">
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65 <assert_contents>
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66 <has_n_lines n="2"/>
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67 <has_text text="iroB,iroC,sinH"/>
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68 </assert_contents>
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69 </output>
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70 </test>
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71 <!-- Multiple samples, no logfile -->
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72 <test expect_num_outputs="4">
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73 <param name="contig" value="NC_003198.1_1kb.fasta,NC_011750.1_1kb.fasta" />
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74 <param name="species" value="Salmonella" />
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75 <param name="identity" value="0.9" />
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76 <param name="log_file" value="false" />
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77 <output name="virulence_summary" ftype="txt">
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78 <assert_contents>
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79 <has_n_lines n="3"/>
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80 </assert_contents>
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81 </output>
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82 </test>
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83 </tests>
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84 <help>
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85 *Taming the AMR beast*
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86
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87 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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88 + Acquired resistance mechanims in the form of point mutations (restricted to subset of species)
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89 + Streamlined output.
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90 + Presence of virulence factors
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91 </help>
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92 <citations>
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93 <citation type="doi">10.5281/zenodo.7370627</citation>
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94 </citations>
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95 </tool>