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comparison staramr_search.xml @ 5:930893c83a1a draft

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planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
author nml
date Tue, 19 Feb 2019 16:47:25 -0500
parents 1e8ec0f861ff
children 3c09557ac425
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4:1e8ec0f861ff 5:930893c83a1a
1 <tool id="staramr_search" name="staramr" version="0.3.0"> 1 <tool id="staramr_search" name="staramr" version="@VERSION@">
2 <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description> 2 <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description>
3 <macros>
4 <token name="@VERSION@">0.4.0</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="0.3.0">staramr</requirement> 7 <requirement type="package" version="@VERSION@">staramr</requirement>
5 </requirements> 8 </requirements>
9 <version_command>staramr --version</version_command>
6 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
7 #import re 11 #import re
8 12
9 #set $named_genomes = '' 13 #set $named_genomes = ''
10 #for $genome in $genomes 14 #for $genome in $genomes
55 <conditional name="use_pointfinder"> 59 <conditional name="use_pointfinder">
56 <param name="enable" type="boolean" label="Enable scanning for point mutations using the PointFinder database" /> 60 <param name="enable" type="boolean" label="Enable scanning for point mutations using the PointFinder database" />
57 <when value="true"> 61 <when value="true">
58 <param name="organism" type="select" label="Select a pointfinder organism"> 62 <param name="organism" type="select" label="Select a pointfinder organism">
59 <option value="salmonella" selected="true">Salmonella</option> 63 <option value="salmonella" selected="true">Salmonella</option>
64 <option value="campylobacter">Campylobacter</option>
60 </param> 65 </param>
61 </when> 66 </when>
62 <when value="false" /> 67 <when value="false" />
63 </conditional> 68 </conditional>
64 <section name="advanced" title="Advanced options" expanded="false"> 69 <section name="advanced" title="Advanced options" expanded="false">
162 167
163 Usage 168 Usage
164 ----- 169 -----
165 170
166 1. Select your genome contigs (in FASTA format). 171 1. Select your genome contigs (in FASTA format).
167 2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* is supported). 172 2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* and *campylobacter* is supported).
168 3. Run the tool. 173 3. Run the tool.
169 174
170 Input 175 Input
171 ----- 176 -----
172 177