Mercurial > repos > dfornika > blast_report_basic

comparison blast_report_basic.xml @ 0:5dfd84907521 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
author dfornika
date Tue, 03 Mar 2020 00:14:34 +0000
parents
children a63f676fe808
comparison
equal deleted inserted replaced
-1:000000000000 0:5dfd84907521
1 <tool id="blast_report_basic" name="BLAST report" version="0.1.0+galaxy0" >
2 <description>Produce an HTML table report of BLAST results</description>
3 <command detect_errors="error_code">
4 <![CDATA[
5 '${__tool_directory__}/blast_report.py'
6 -f ${filter_pident}:$filter_kws
7 #if str($bins) != "None"
8 -b "${bins}"
9 #end if
10 $discard_redundant
11 '${tabular_blast_report_input}'
12 '${__tool_directory__}/templates/template2.tmpl}'
13 '${out_html}'
14 '${out_tab}'
15 ]]>
16 </command>
17 <inputs>
18 <param name="tabular_blast_report_input" type="data" format="tabular" label="Tabular BLAST results (extended 26 columns)"/>
19 <param name="filter_pident" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
20 <param name="filter_kws" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
21 <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes">
22 <options from_data_table="blast_reference_bins">
23 <validator type="no_options" message="No BLAST reference bins available" />
24 </options>
25 </param>
26 <param name="discard_redundant" type="boolean" truevalue="-r" falsevalue="" label="Throw out redundant hits?"/>
27 </inputs>
28 <outputs>
29 <data name="out_html" format="html" label="$tool.name on data $in_tab.hid: report"/>
30 <data name="out_tab" format="tabular" label="$tool.name on data $in_tab.hid: tabular results"/>
31 </outputs>
32 <help>
33
34 .. class:: infomark
35
36 **What it does**
37
38 This tool produces a HTML report for each query in a tabular BLAST file.
39
40 ----
41
42 **Tabular BLAST results**
43
44 One or more query's BLAST results in extended 26 column tabular format.
45
46 ----
47
48 **Report template**
49
50 The report template dictates the format of the HTML report.
51 Note that changing the template from the standard "Top 20 hits shown, toggle remainder" to "Euzby results shown first" causes
52 the order of the results in the HTML report and the tabular BLAST results (if outputted) to be inconsistent with each other.
53
54 ----
55
56 **Minimum percentage identity**
57
58 Filter by percentage identity. This filter is applied before the description keyword filters.
59
60 ----
61
62 **Comma-separated list of description keyword filters**
63
64 Filter by description keywords. Do not include spaces (unless your keyword is two words). These are applied
65 after the percentage identity filter.
66
67 ----
68
69 **Database bins**
70
71 Bin the results by accession number into "database bins."
72
73 ----
74
75 **Throw out redundant hits?**
76
77 Only the first hit for any accession number will be reported.
78
79 ----
80
81 **Output tabular BLAST results?**
82
83 This option produces a tabular BLAST file with the same results as those shown in the report.
84
85 </help>
86 </tool>