Mercurial > repos > diodupima > phage_coast_search

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
author diodupima
date Wed, 17 Nov 2021 11:11:00 +0000
parents fb0ce7937a85
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
1 <tool id="phage_coast_search" name="PhageCOAST - Search" version="0.2.0">
0
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
2 <description>Run a new job, and identify the closest proteomes</description>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
3 <macros>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
4 <import>macros.xml</import>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
5 </macros>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
6 <requirements>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
7 <expand macro="requirements"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
8 </requirements>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
9 <command><![CDATA[
1
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
10 coast search
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
11 "$db"
0
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
12 @QUERY@
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
13 --engine blast
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
14 --inplace_workspace
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
15 @QUERY_KEYWORDS@
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
16 @BLAST_TAX_FILTER@
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
17 @BLAST_ALN_OPTIONS@
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
18 @GENERIC_ALN_OPTIONS@
1
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
19 --web 'http://rosalind.di.uminho.pt:6082/'
0
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
20 --email phage@coast.um
1
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
21 && coast report
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
22 "blast_results.tab"
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
23 @QUERY@
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
24 @AAI_FILTER@
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
25 @OUTPUT_FORMAT@
6a33bad2db7f "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
diodupima
parents: 0
diff changeset
26 @QUERY_KEYWORDS@
0
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
27 ]]></command>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
28 <inputs>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
29 <expand macro="input_query" />
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
30 <expand macro="merlin_db_selection"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
31 <expand macro="blast_taxon_filter"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
32 <expand macro="output_format"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
33 <expand macro="aai_filter"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
34 <section name="aln_adv" title="Advanced Alignment Settings" >
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
35 <expand macro="blast_aln_options"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
36 <expand macro="generic_aln_options"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
37 </section>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
38 </inputs>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
39 <outputs>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
40 <expand macro="results_alignment"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
41 <expand macro="results_report"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
42 </outputs>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
43 <tests>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
44 </tests>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
45 <help>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
46
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
47 @TIME_WARNING@
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
48
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
49 PhageCOAST
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
50 ==========
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
51
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
52 @GENERAL_DESC@
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
53
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
54 PhageCOAST is COAST adapted for the Phage Toolkit. The current build uses BLASTp as the search backend tool.
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
55
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
56 @AAI_DESC@
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
57 @TAX_FILTER_WARNING@
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
58 @OUT_DESC@
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
59
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
60 </help>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
61 <citations>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
62 <expand macro="citations_coast"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
63 <expand macro="citations_blast"/>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
64 </citations>
fb0ce7937a85 "planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diodupima
parents:
diff changeset
65 </tool>