Mercurial > repos > iuc > argnorm

annotate argnorm.xml @ 0:26168d6b86f2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
author iuc
date Wed, 28 Aug 2024 20:27:07 +0000
parents
children 82c355310c7b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
1 <tool id="argnorm" name="argNorm" version="@VERSION@+galaxy0" profile="22.05">
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
2 <description>a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO)</description>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
3 <macros>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
4 <token name="@VERSION@">0.6.0</token>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
5 </macros>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
6 <xrefs>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
7 <xref type="bio.tools">argnorm</xref>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
8 </xrefs>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
9 <requirements>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
10 <requirement type="package" version="@VERSION@">argnorm</requirement>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
11 </requirements>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
13 argnorm
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
14 '$tool'
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
15 --db '$db'
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
16 -i '$input'
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
17 -o '$output'
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
18 $hamronized
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
19 ]]></command>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
20 <inputs>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
21 <param type="data" name="input" format="tsv,txt" label="Specify input file" help="-i" />
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
22 <param type="select" name="tool" label="The tool you used to do ARG annotation" help="[tool]" >
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
23 <option value="deeparg" selected="true">DeepARG</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
24 <option value="argsoap">ARGs_OAP</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
25 <option value="abricate">ABRicate</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
26 <option value="resfinder">ResFinder</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
27 <option value="amrfinderplus">AMRFinderPlus</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
28 <option value="groot">Groot</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
29 </param>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
30 <param type="select" argument="--db" label="The database you used to do ARG annotation">
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
31 <option value="sarg" selected="true">SARG</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
32 <option value="ncbi">NCBI</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
33 <option value="resfinder">ResFinder</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
34 <option value="deeparg" selected="true">DeepARG</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
35 <option value="amrfinderplus">AMRFinderPlus</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
36 <option value="megares">MEGARes</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
37 <option value="argannot">ARG-ANNOT</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
38 <option value="groot-resfinder">Groot ResFinder database </option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
39 <option value="groot-argannot">Groot ARG-ANNOT database </option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
40 <option value="groot-card">Groot CARD database </option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
41 <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
42 <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
43 </param>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
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)" />
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
45 </inputs>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
46 <outputs>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
47 <data name="output" format="tsv" label="${tool.name} on ${on_string} : ARG normalized table" />
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
48 </outputs>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
49 <tests>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
50 <!-- Test 1 : input : tsv, output : tsv, tool : groot -->
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
51 <test>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
52 <param name="input" value="resfinder_PSM7J199_R2.report"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
53 <param name="tool" value="groot"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
54 <param name="db" value="groot-resfinder"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
55 <output name="output" file="groot-resfinder-results.tsv"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
56 </test>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
57 <!-- Test 2 : input : txt, output : tsv, tool : argsoap -->
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
58 <test>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
59 <param name="input" value="blastout.filtered.txt"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
60 <param name="tool" value="argsoap"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
61 <param name="db" value="sarg"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
62 <output name="output" file="blastout.filtered.argnorm.tsv"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
63 </test>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
64 <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize : true -->
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
65 <test>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
66 <param name="input" value="deeparg_hamronize.tsv"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
67 <param name="tool" value="deeparg"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
68 <param name="db" value="deeparg"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
69 <param name="hamronized" value="true"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
70 <output name="output" file="deeparg_hamronize_argnorm_results.tsv"/>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
71 </test>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
72 </tests>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
73 <help><![CDATA[
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
74
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
75 argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
76
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
77 argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
78
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
79 ]]></help>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
80 <citations>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
81 <citation type="doi">https://github.com/BigDataBiology/argNorm</citation>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
82 </citations>
26168d6b86f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
iuc
parents:
diff changeset
83 </tool>