Mercurial > repos > diodupima > phage_coast_search

comparison phage_coast_search.xml @ 1:6a33bad2db7f draft default tip

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"planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
author diodupima
date Wed, 17 Nov 2021 11:11:00 +0000
parents fb0ce7937a85
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0:fb0ce7937a85 1:6a33bad2db7f
1 <tool id="phage_coast_search" name="PhageCOAST - Search" version="0.1.2"> 1 <tool id="phage_coast_search" name="PhageCOAST - Search" version="0.2.0">
2 <description>Run a new job, and identify the closest proteomes</description> 2 <description>Run a new job, and identify the closest proteomes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 </requirements> 8 </requirements>
9 <command><![CDATA[ 9 <command><![CDATA[
10 coast 10 coast search
11 "$db"
11 @QUERY@ 12 @QUERY@
12 "$db"
13 --engine blast 13 --engine blast
14 --inplace_workspace 14 --inplace_workspace
15 @AAI_FILTER@
16 @OUTPUT@
17 @QUERY_KEYWORDS@ 15 @QUERY_KEYWORDS@
18 @OUTPUT_FORMAT@
19 @BLAST_TAX_FILTER@ 16 @BLAST_TAX_FILTER@
20 @BLAST_ALN_OPTIONS@ 17 @BLAST_ALN_OPTIONS@
21 @GENERIC_ALN_OPTIONS@ 18 @GENERIC_ALN_OPTIONS@
22 -w 'http://rosalind.di.uminho.pt:6082/' 19 --web 'http://rosalind.di.uminho.pt:6082/'
23 --email phage@coast.um 20 --email phage@coast.um
21 && coast report
22 "blast_results.tab"
23 @QUERY@
24 @AAI_FILTER@
25 @OUTPUT_FORMAT@
26 @QUERY_KEYWORDS@
24 ]]></command> 27 ]]></command>
25 <inputs> 28 <inputs>
26 <expand macro="input_query" /> 29 <expand macro="input_query" />
27 <expand macro="merlin_db_selection"/> 30 <expand macro="merlin_db_selection"/>
28 <expand macro="blast_taxon_filter"/> 31 <expand macro="blast_taxon_filter"/>