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comparison cpo_clustalw.xml @ 5:698579246d0d draft

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planemo upload
author jjjjia
date Tue, 21 Aug 2018 17:53:08 -0400
parents fea89c4d5227
children cabceaa239e4
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4:bd6f5844d60e 5:698579246d0d
1 <tool id="cpo_clustalw" name="cpo_clustalw" version="2.1"> 1 <tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
2 <description>makes tree from alignment</description> 2 <description>Modified version of clustalw2 v2.1 to produce NJ trees from an SNIPPY produced alignment</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1">clustalw</requirement> 4 <requirement type="package" version="2.1">clustalw</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
7 <![CDATA[ 7 <![CDATA[
13 </inputs> 13 </inputs>
14 <outputs> 14 <outputs>
15 <data name="phylip" format="txt" from_work_dir="*.ph"/> 15 <data name="phylip" format="txt" from_work_dir="*.ph"/>
16 <data name="njtree" format="txt" from_work_dir="*.nj*"/> 16 <data name="njtree" format="txt" from_work_dir="*.nj*"/>
17 </outputs> 17 </outputs>
18 <tests>
19 <test>
20 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
21 <section name="adv_param">
22 <param name="evalue" value="0.00001"/>
23 <param name="unicycler_contigs" value="True"/>
24 <param name="run_circlator" value="True"/>
25 </section>
26 <output name="outfile1">
27 <assert_contents>
28 <has_text text="NC_019097"/>
29 </assert_contents>
30 </output>
31 </test>
32 </tests>
33 <help> 18 <help>
34 19
35 **Syntax** 20 **Syntax**
36 21
37 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases. 22 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.