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comparison coast_report.xml @ 0:44bd59ba0858 draft

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"planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
author diodupima
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>