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comparison 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
children
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4:e909d3bc4687 5:468fd92deaaa
1 <tool id="abritamr" name="abriTAMR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="abritamr" name="abriTAMR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>AMR gene detection with AMRFinderPlus</description> 2 <description>AMR gene detection with AMRFinderPlus</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0.19</token> 4 <token name="@TOOL_VERSION@">1.0.19</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <token name="@PROFILE@">22.05</token> 6 <token name="@PROFILE@">22.05</token>
7 </macros> 7 </macros>
8 <xrefs> 8 <xrefs>
9 <xref type="bio.tools">abritamr</xref> 9 <xref type="bio.tools">abritamr</xref>
10 </xrefs> 10 </xrefs>
49 </param> 49 </param>
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."/> 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."/>
51 <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/> 51 <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/>
52 </inputs> 52 </inputs>
53 <outputs> 53 <outputs>
54 <data name="abriTAMR_output" format="txt" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" /> 54 <data name="abriTAMR_output" format="tabular" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" />
55 <data name="matches_summary" format="txt" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/> 55 <data name="matches_summary" format="tabular" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/>
56 <data name="partials_summary" format="txt" label="${tool.name} on ${on_string}: partials summary" from_work_dir="summary_partials.txt"/> 56 <data name="partials_summary" format="tabular" label="${tool.name} on ${on_string}: partials summary" from_work_dir="summary_partials.txt"/>
57 <data name="virulence_summary" format="txt" label="${tool.name} on ${on_string}: virulence summary" from_work_dir="summary_virulence.txt"/> 57 <data name="virulence_summary" format="tabular" label="${tool.name} on ${on_string}: virulence summary" from_work_dir="summary_virulence.txt"/>
58 <data name="log" format="txt" label="${tool.name} on ${on_string}: log file" from_work_dir="abritamr.log"> 58 <data name="log" format="txt" label="${tool.name} on ${on_string}: log file" from_work_dir="abritamr.log">
59 <filter>log_file</filter> 59 <filter>log_file</filter>
60 </data> 60 </data>
61 </outputs> 61 </outputs>
62 <tests> 62 <tests>
63 <!-- Single sample, with logfile --> 63 <!-- Single sample, with logfile -->
64 <test expect_num_outputs="5"> 64 <test expect_num_outputs="5">
65 <param name="contig" value="CP009102.1.fasta" /> 65 <param name="contig" value="CP009102.1.fasta" />
66 <param name="log_file" value="true" /> 66 <param name="log_file" value="true" />
67 <output name="virulence_summary" ftype="txt"> 67 <output name="virulence_summary" ftype="tabular">
68 <assert_contents> 68 <assert_contents>
69 <has_n_lines n="2"/> 69 <has_n_lines n="2"/>
70 <has_text text="sinH"/> 70 <has_text text="sinH"/>
71 <has_n_columns n="2"/>
71 </assert_contents> 72 </assert_contents>
72 </output> 73 </output>
73 </test> 74 </test>
74 <!-- Multiple samples, no logfile --> 75 <!-- Multiple samples, no logfile -->
75 <test expect_num_outputs="4"> 76 <test expect_num_outputs="4">
76 <param name="contig" value="NC_003198.1_1kb.fasta,NC_011750.1_1kb.fasta" /> 77 <param name="contig" value="NC_003198.1_1kb.fasta,NC_011750.1_1kb.fasta" />
77 <param name="species" value="Salmonella" /> 78 <param name="species" value="Salmonella" />
78 <param name="identity" value="0.9" /> 79 <param name="identity" value="0.9" />
79 <param name="log_file" value="false" /> 80 <param name="log_file" value="false" />
80 <output name="virulence_summary" ftype="txt"> 81 <output name="virulence_summary" ftype="tabular">
81 <assert_contents> 82 <assert_contents>
82 <has_n_lines n="3"/> 83 <has_n_lines n="3"/>
83 <has_text text="NC_003198.1_1kb.fasta"/> 84 <has_text text="NC_003198.1_1kb.fasta"/>
85 <has_n_columns n="1"/>
84 </assert_contents> 86 </assert_contents>
85 </output> 87 </output>
86 </test> 88 </test>
87 </tests> 89 </tests>
88 <help> 90 <help>