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comparison phage_coast_search.xml @ 0:fb0ce7937a85 draft

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"planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
author diodupima
date Thu, 15 Jul 2021 16:51:26 +0000
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1 <tool id="phage_coast_search" name="PhageCOAST - Search" version="0.1.2">
2 <description>Run a new job, and identify the closest proteomes</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <expand macro="requirements"/>
8 </requirements>
9 <command><![CDATA[
10 coast
11 @QUERY@
12 "$db"
13 --engine blast
14 --inplace_workspace
15 @AAI_FILTER@
16 @OUTPUT@
17 @QUERY_KEYWORDS@
18 @OUTPUT_FORMAT@
19 @BLAST_TAX_FILTER@
20 @BLAST_ALN_OPTIONS@
21 @GENERIC_ALN_OPTIONS@
22 -w 'http://rosalind.di.uminho.pt:6082/'
23 --email phage@coast.um
24 ]]></command>
25 <inputs>
26 <expand macro="input_query" />
27 <expand macro="merlin_db_selection"/>
28 <expand macro="blast_taxon_filter"/>
29 <expand macro="output_format"/>
30 <expand macro="aai_filter"/>
31 <section name="aln_adv" title="Advanced Alignment Settings" >
32 <expand macro="blast_aln_options"/>
33 <expand macro="generic_aln_options"/>
34 </section>
35 </inputs>
36 <outputs>
37 <expand macro="results_alignment"/>
38 <expand macro="results_report"/>
39 </outputs>
40 <tests>
41 </tests>
42 <help>
43
44 @TIME_WARNING@
45
46 PhageCOAST
47 ==========
48
49 @GENERAL_DESC@
50
51 PhageCOAST is COAST adapted for the Phage Toolkit. The current build uses BLASTp as the search backend tool.
52
53 @AAI_DESC@
54 @TAX_FILTER_WARNING@
55 @OUT_DESC@
56
57 </help>
58 <citations>
59 <expand macro="citations_coast"/>
60 <expand macro="citations_blast"/>
61 </citations>
62 </tool>