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comparison 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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-1:000000000000 0:6085c9fbda49
1 <tool id="abritamr" name="abriTAMR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>AMR gene detection with AMRFinderPlus</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.14</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@PROFILE@">22.05</token>
7 </macros>
8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">abritamr</requirement>
10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[
12 abritamr run
13 --contigs '$input_tsv'
14 #if $species:
15 --species '$species'
16 #end if
17 #if $identity:
18 --identity '$identity'
19 #end if
20 --jobs \${GALAXY_SLOTS:-4}
21 ]]></command>
22 <configfiles>
23 <configfile name="input_tsv">
24 #for $i in $contig:
25 ${i.element_identifier} ${i}
26 #end for
27 </configfile>
28 </configfiles>
29 <inputs>
30 <param name="contig" type="data" format="fasta" multiple="true" label="Input contigs"/>
31 <param argument="species" type="select" multiple="false" optional="true" label="Specify species to aquire resistance mechanisms as point mutations">
32 <option value="Neisseria">Neisseria</option>
33 <option value="Clostridioides_difficile">Clostridioides difficile</option>
34 <option value="Acinetobacter_baumannii">Acinetobacter baumannii</option>
35 <option value="Campylobacter">Campylobacter</option>
36 <option value="Enterococcus_faecalis">Enterococcus faecalis</option>
37 <option value="Enterococcus_faecium">Enterococcus faecium</option>
38 <option value="Escherichia">Escherichia</option>
39 <option value="Klebsiella">Klebsiella</option>
40 <option value="Salmonella">Salmonella</option>
41 <option value="Staphylococcus_aureus">Staphylococcus aureus</option>
42 <option value="Staphylococcus_pseudintermedius">Staphylococcus pseudintermedius</option>
43 <option value="Streptococcus_agalactiae">Streptococcus agalactiae</option>
44 <option value="Streptococcus_pneumoniae">Streptococcus pneumoniae</option>
45 <option value="Streptococcus_pyogenes">Streptococcus pyogenes</option>
46 </param>
47 <param argument="identity" value="0.9" type="float" optional="true" min="0.0" max="1" label="Minimum identity of matches with armfinder. Default: 0.9, unless curated threshold is present for the gene."/>
48 <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/>
49 </inputs>
50 <outputs>
51 <data name="abriTAMR_output" format="txt" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" />
52 <data name="matches_summary" format="txt" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/>
53 <data name="partials_summary" format="txt" label="${tool.name} on ${on_string}: partials summary" from_work_dir="summary_partials.txt"/>
54 <data name="virulence_summary" format="txt" label="${tool.name} on ${on_string}: virulence summary" from_work_dir="summary_virulence.txt"/>
55 <data name="log" format="txt" label="${tool.name} on ${on_string}: log file" from_work_dir="abritamr.log">
56 <filter>log_file</filter>
57 </data>
58 </outputs>
59 <tests>
60 <!-- Single sample, with logfile -->
61 <test expect_num_outputs="5">
62 <param name="contig" value="CP009102.1.fasta" />
63 <param name="log_file" value="true" />
64 <output name="virulence_summary" ftype="txt">
65 <assert_contents>
66 <has_n_lines n="2"/>
67 <has_text text="iroB,iroC,sinH"/>
68 </assert_contents>
69 </output>
70 </test>
71 <!-- Multiple samples, no logfile -->
72 <test expect_num_outputs="4">
73 <param name="contig" value="NC_003198.1_1kb.fasta,NC_011750.1_1kb.fasta" />
74 <param name="species" value="Salmonella" />
75 <param name="identity" value="0.9" />
76 <param name="log_file" value="false" />
77 <output name="virulence_summary" ftype="txt">
78 <assert_contents>
79 <has_n_lines n="3"/>
80 </assert_contents>
81 </output>
82 </test>
83 </tests>
84 <help>
85 *Taming the AMR beast*
86
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.
88 + Acquired resistance mechanims in the form of point mutations (restricted to subset of species)
89 + Streamlined output.
90 + Presence of virulence factors
91 </help>
92 <citations>
93 <citation type="doi">10.5281/zenodo.7370627</citation>
94 </citations>
95 </tool>