Mercurial > repos > diodupima > coast_report

annotate coast_report.xml @ 0:44bd59ba0858 draft

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