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comparison abritamr.xml @ 1:f564aae1b543 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit f681189e570539c9489d42f2ab1fac6f3a8ef342
author iuc
date Fri, 10 Nov 2023 20:28:10 +0000
parents 6085c9fbda49
children 3719342715a8
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0:6085c9fbda49 1:f564aae1b543
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@">1.0.14</token> 4 <token name="@TOOL_VERSION@">1.0.14</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 <requirements> 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">abritamr</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">abritamr</requirement>
10 </requirements> 10 </requirements>
42 <option value="Staphylococcus_pseudintermedius">Staphylococcus pseudintermedius</option> 42 <option value="Staphylococcus_pseudintermedius">Staphylococcus pseudintermedius</option>
43 <option value="Streptococcus_agalactiae">Streptococcus agalactiae</option> 43 <option value="Streptococcus_agalactiae">Streptococcus agalactiae</option>
44 <option value="Streptococcus_pneumoniae">Streptococcus pneumoniae</option> 44 <option value="Streptococcus_pneumoniae">Streptococcus pneumoniae</option>
45 <option value="Streptococcus_pyogenes">Streptococcus pyogenes</option> 45 <option value="Streptococcus_pyogenes">Streptococcus pyogenes</option>
46 </param> 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."/> 47 <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."/>
48 <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/> 48 <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/>
49 </inputs> 49 </inputs>
50 <outputs> 50 <outputs>
51 <data name="abriTAMR_output" format="txt" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" /> 51 <data name="abriTAMR_output" format="txt" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" />
52 <data name="matches_summary" format="txt" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/> 52 <data name="matches_summary" format="txt" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/>