Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_mash.xml @ 18:596bf8a792de draft

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author jjjjia
date Tue, 28 Aug 2018 15:15:09 -0400
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children 47502be81f6a
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17:ed3b291693fc 18:596bf8a792de
1 <tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
2 <description>Modified version of mash 2.0 with custom database</description>
3 <requirements>
4 <requirement type="package" version="2.0">mash</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8 mash screen $__tool_directory__/bcPlasmidDB.msh $input | sort -gr | head -10 > mashresult.tsv
9 ]]>
10 </command>
11 <inputs>
12 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
13 </inputs>
14 <outputs>
15 <data name="mashResult" format="tabular" from_work_dir="mashresult.tsv"/>
16 </outputs>
17 <help>
18 mash screen bcPlasmidDB.msh $input | sort -gr | head -10 > mashresult.tsv
19 </help>
20 <citations>
21 <citation type="bibtex">
22 @misc{githubmob-suite,
23 author = {Robertson J, Nash J},
24 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
25 publisher = {GitHub},
26 journal = {GitHub repository},
27 doi = {10.1099/mgen.0.000206},
28 url = {https://github.com/phac-nml/mob-suite}
29 }</citation>
30 </citations>
31 </tool>