Mercurial > repos > diodupima > coast_report
comparison coast_report.xml @ 0:44bd59ba0858 draft
"planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
author | diodupima |
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date | Thu, 15 Jul 2021 16:52:36 +0000 |
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children | 3f1f00433c2b |
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1 <tool id="coast_report" name="COAST - Report generator" version="0.1.2"> | |
2 <description>Recreate the report and outputs with different settings</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <requirements> | |
7 <expand macro="requirements"/> | |
8 </requirements> | |
9 <command><![CDATA[ | |
10 coast_report | |
11 @QUERY@ | |
12 "$result_file" | |
13 @AAI_FILTER@ | |
14 @HYPO_FILTER@ | |
15 @OUTPUT@ | |
16 @QUERY_KEYWORDS@ | |
17 @OUTPUT_FORMAT@ | |
18 ]]></command> | |
19 <inputs> | |
20 <!--Select the kind of input to be used--> | |
21 <expand macro="input_query" /> | |
22 <param name="result_file" type="data" format="tabular" label="Load previous COAST generated alignment file"/> | |
23 <!--Outputs selection--> | |
24 <expand macro="output_format"/> | |
25 <!--AAI filtering score--> | |
26 <expand macro="aai_filter"/> | |
27 <expand macro="hypothetical_filter"/> | |
28 </inputs> | |
29 <outputs> | |
30 <expand macro="results_report"/> | |
31 </outputs> | |
32 <tests> | |
33 <test> | |
34 <param name="query_file" value="protein.faa" /> | |
35 <param name="result_file" value="blast_results.tab" /> | |
36 <param name="aai" value="10" /> | |
37 <param name="min_cov" value="50" /> | |
38 <param name="min_id" value="40" /> | |
39 <output name="coast_report" file="report/coast_report.html" lines_diff="4"/> | |
40 <output name="bh_results" file="report/bh_results.tab" /> | |
41 <output name="coast_results" file="report/coast_results.tab" /> | |
42 </test> | |
43 <test> | |
44 <param name="query_file" value="protein.faa" /> | |
45 <param name="result_file" value="blast_results.tab" /> | |
46 <param name="aai" value="20" /> | |
47 <param name="min_cov" value="30" /> | |
48 <param name="min_id" value="30" /> | |
49 <param name="hypothetical" value="true" /> | |
50 <output name="coast_report" file="report_h/coast_report.html" lines_diff="4"/> | |
51 <output name="bh_results" file="report_h/bh_results.tab" /> | |
52 <output name="coast_results" file="report_h/coast_results.tab" /> | |
53 </test> | |
54 </tests> | |
55 <help> | |
56 | |
57 @HYPO_FILTER_WARNING@ | |
58 | |
59 COAST Report | |
60 ============ | |
61 | |
62 Generate COAST reports and outputs based in different parameters, using the tabular alignment output produced by COAST Search jobs. | |
63 | |
64 @GENERAL_DESC@ | |
65 @AAI_DESC@ | |
66 @OUT_DESC@ | |
67 | |
68 </help> | |
69 <citations> | |
70 <expand macro="citations_coast"/> | |
71 </citations> | |
72 </tool> |