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comparison argnorm.xml @ 1:82c355310c7b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit 4de98d11ef4e46d92c545f665499be8fd714bac5
author iuc
date Wed, 23 Apr 2025 09:04:17 +0000
parents 26168d6b86f2
children
comparison
equal deleted inserted replaced
0:26168d6b86f2 1:82c355310c7b
1 <tool id="argnorm" name="argNorm" version="@VERSION@+galaxy0" profile="22.05"> 1 <tool id="argnorm" name="argNorm" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO)</description> 2 <description>a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO)</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.6.0</token> 4 <token name="@VERSION@">1.0.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
5 </macros> 6 </macros>
6 <xrefs> 7 <xrefs>
7 <xref type="bio.tools">argnorm</xref> 8 <xref type="bio.tools">argnorm</xref>
8 </xrefs> 9 </xrefs>
9 <requirements> 10 <requirements>
10 <requirement type="package" version="@VERSION@">argnorm</requirement> 11 <requirement type="package" version="@VERSION@">argnorm</requirement>
11 </requirements> 12 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
13 argnorm 14 argnorm
14 '$tool' 15 '$choose_tool.tool'
16 #if $choose_tool.tool == "abricate" or $choose_tool.tool == "groot"
15 --db '$db' 17 --db '$db'
18 #end if
16 -i '$input' 19 -i '$input'
17 -o '$output' 20 -o '$output'
21 #if $choose_tool.tool == "hamronization"
18 $hamronized 22 $hamronized
23 #end if
19 ]]></command> 24 ]]></command>
20 <inputs> 25 <inputs>
21 <param type="data" name="input" format="tsv,txt" label="Specify input file" help="-i" /> 26 <param type="data" name="input" format="tsv,txt" label="Specify input file" help="-i" />
22 <param type="select" name="tool" label="The tool you used to do ARG annotation" help="[tool]" > 27 <conditional name="choose_tool">
23 <option value="deeparg" selected="true">DeepARG</option> 28 <param type="select" name="tool" label="The tool used to do ARG annotation" help="" >
24 <option value="argsoap">ARGs_OAP</option> 29 <option value="deeparg" selected="true">DeepARG</option>
25 <option value="abricate">ABRicate</option> 30 <option value="argsoap">ARGs-OAP</option>
26 <option value="resfinder">ResFinder</option> 31 <option value="abricate">ABRicate</option>
27 <option value="amrfinderplus">AMRFinderPlus</option> 32 <option value="resfinder">ResFinder</option>
28 <option value="groot">Groot</option> 33 <option value="amrfinderplus">AMRFinderPlus</option>
29 </param> 34 <option value="groot">Groot</option>
30 <param type="select" argument="--db" label="The database you used to do ARG annotation"> 35 <option value="hamronization">hAMRonization</option>
31 <option value="sarg" selected="true">SARG</option> 36 </param>
32 <option value="ncbi">NCBI</option> 37 <when value="deeparg">
33 <option value="resfinder">ResFinder</option> 38 </when>
34 <option value="deeparg" selected="true">DeepARG</option> 39 <when value="argsoap">
35 <option value="amrfinderplus">AMRFinderPlus</option> 40 </when>
36 <option value="megares">MEGARes</option> 41 <when value="abricate">
37 <option value="argannot">ARG-ANNOT</option> 42 <param type="select" argument="--db" label="The database you used to do ARG annotation">
38 <option value="groot-resfinder">Groot ResFinder database </option> 43 <option value="sarg" selected="true">SARG</option>
39 <option value="groot-argannot">Groot ARG-ANNOT database </option> 44 <option value="ncbi">NCBI</option>
40 <option value="groot-card">Groot CARD database </option> 45 <option value="resfinder">ResFinder</option>
41 <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option> 46 <option value="resfinderfg">ResFinder FG</option>
42 <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option> 47 <option value="deeparg" selected="true">DeepARG</option>
43 </param> 48 <option value="megares">MEGARes</option>
44 <param name="hamronized" type="boolean" label="If the input is hamronized" truevalue="--hamronized" falsevalue="" optional="true" help="Use this if the input is hamronized (processed using the hAMRonization tool)" /> 49 <option value="argannot">ARG-ANNOT</option>
50 </param>
51 </when>
52 <when value="resfinder">
53 </when>
54 <when value="amrfinderplus">
55 </when>
56 <when value="groot">
57 <param type="select" argument="--db" label="The database you used to do ARG annotation">
58 <option value="groot-resfinder">Groot ResFinder database </option>
59 <option value="groot-argannot">Groot ARG-ANNOT database </option>
60 <option value="groot-card">Groot CARD database </option>
61 <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option>
62 <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option>
63 </param>
64 </when>
65 <when value="hamronization">
66 <param name="hamronized" type="boolean" label="Skip rows with unsupported tools" truevalue="--hamronization_skip_unsupported_tool" falsevalue="" checked="false" help="Combined hAMRonization results can have ARGs detected by unsupported tools (e.g. staramr), --hamronization_skip_unsupported_tool allows to skip rows with unsupported tools"/>
67 </when>
68 </conditional>
45 </inputs> 69 </inputs>
46 <outputs> 70 <outputs>
47 <data name="output" format="tsv" label="${tool.name} on ${on_string} : ARG normalized table" /> 71 <data name="output" format="tsv" label="${tool.name} on ${on_string} : ARG normalized table" />
48 </outputs> 72 </outputs>
49 <tests> 73 <tests>
50 <!-- Test 1 : input : tsv, output : tsv, tool : groot --> 74 <!-- Test 1 : input : tsv, output : tsv, tool : groot -->
51 <test> 75 <test>
52 <param name="input" value="resfinder_PSM7J199_R2.report"/> 76 <param name="input" value="resfinder_PSM7J199_R2.report"/>
53 <param name="tool" value="groot"/> 77 <conditional name="choose_tool">
54 <param name="db" value="groot-resfinder"/> 78 <param name="tool" value="groot"/>
79 <param name="db" value="groot-resfinder"/>
80 </conditional>
55 <output name="output" file="groot-resfinder-results.tsv"/> 81 <output name="output" file="groot-resfinder-results.tsv"/>
56 </test> 82 </test>
57 <!-- Test 2 : input : txt, output : tsv, tool : argsoap --> 83 <!-- Test 2 : input : txt, output : tsv, tool : argsoap -->
58 <test> 84 <test>
59 <param name="input" value="blastout.filtered.txt"/> 85 <param name="input" value="blastout.filtered.txt"/>
60 <param name="tool" value="argsoap"/> 86 <conditional name="choose_tool">
61 <param name="db" value="sarg"/> 87 <param name="tool" value="argsoap"/>
88 </conditional>
62 <output name="output" file="blastout.filtered.argnorm.tsv"/> 89 <output name="output" file="blastout.filtered.argnorm.tsv"/>
63 </test> 90 </test>
64 <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize : true --> 91 <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize -->
65 <test> 92 <test>
66 <param name="input" value="deeparg_hamronize.tsv"/> 93 <param name="input" value="deeparg_hamronize.tsv"/>
67 <param name="tool" value="deeparg"/> 94 <conditional name="choose_tool">
68 <param name="db" value="deeparg"/> 95 <param name="tool" value="hamronization"/>
69 <param name="hamronized" value="true"/> 96 <param name="hamronized" value="true"/>
97 </conditional>
70 <output name="output" file="deeparg_hamronize_argnorm_results.tsv"/> 98 <output name="output" file="deeparg_hamronize_argnorm_results.tsv"/>
71 </test> 99 </test>
72 </tests> 100 </tests>
73 <help><![CDATA[ 101 <help><![CDATA[
74 102