Mercurial > repos > estrain > amrfinderplus_db

comparison macro.xml @ 0:06165bd8c9a0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8
author estrain
date Thu, 12 Mar 2026 18:53:36 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:06165bd8c9a0
1 <macros>
2 <token name="@TOOL_VERSION@">4.2.5</token>
3 <token name="@VERSION_SUFFIX@">2</token>
4 <token name="@PROFILE@">21.05</token>
5 <xml name="version_command">
6 <version_command><![CDATA[amrfinder --version]]></version_command>
7 </xml>
8 <xml name="biotools">
9 <xrefs>
10 <xref type="bio.tools">amrfinderplus</xref>
11 </xrefs>
12 </xml>
13 <xml name="requirements">
14 <requirements>
15 <requirement type="package" version="@TOOL_VERSION@">ncbi-amrfinderplus</requirement>
16 </requirements>
17 </xml>
18 <xml name="citations">
19 <citations>
20 <citation type="doi">10.1038/s41598-021-91456-0</citation>
21 </citations>
22 </xml>
23
24 <xml name="nucl_input" token_option="">
25 <param name="nucleotide_input" type="data" optional="@OPTION@" format="fasta" label="Input nucleotide sequence file" help="Select the nucleotide sequence file to be analyzed"/>
26 </xml>
27 <xml name="prot_input" token_option="">
28 <param name="protein_input" type="data" optional="@OPTION@" format="fasta" label="Input protein sequence file" help="Select the protein sequence file to be analyzed"/>
29 </xml>
30 <xml name="annotation_type" token_option="">
31 <param name="gff_annotation" type="data" format="gff3" optional="@OPTION@" multiple="false" label="GFF file for protein locations" help="Protein id should be in the attribute Name=id (9th field) of the rows with type CDS or gene (3rd field)"/>
32 <param argument="--annotation_format" type="select" optional="@OPTION@" label="Annotation file format" help="Select the annotation format type (eg. bakta or prokka tool, genbank format (default: genbank)">
33 <option value="bakta">Bakta</option>
34 <option value="genbank">Genbank</option>
35 <option value="microscope">Microscope</option>
36 <option value="patric">Patric</option>
37 <option value="prokka">Prokka</option>
38 <option value="pseudomonasdb">Pseudomonasdb</option>
39 <option value="rast">Rast</option>
40 <option value="standard">Standard</option>
41 <option value="prodigal">Prodigal</option>
42 </param>
43 </xml>
44 </macros>