Mercurial > repos > dfornika > blast_report_basic

comparison blast_report_basic.xml @ 6:b8a3578b6445 draft

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author dfornika
date Tue, 03 Mar 2020 05:33:55 +0000
parents 7223a2e98bf8
children 6650fe4db541
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5:c7ce2cd96546 6:b8a3578b6445
1 <tool id="blast_report_basic" name="BLAST report" version="0.1.0+galaxy0" > 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> 2 <description>Produce an HTML table report of BLAST results</description>
3 <command> 3 <command>
4 <![CDATA[ 4 <![CDATA[
5 python '${__tool_directory__}/blast_report.py' 5 python '${__tool_directory__}/blast_report.py'
6 -f ${filter_pident}:$filter_kws 6 --min-identity ${min_identity}
7 --filter-keywords '${filter_kws}'
7 #if str($bins) != "None" 8 #if str($bins) != "None"
8 -b "${bins}" 9 -b '${bins}'
9 #end if 10 #end if
10 $discard_redundant 11 $discard_redundant
11 '${tabular_blast_report_input}' 12 '${tabular_blast_report_input}'
12 '${__tool_directory__}/templates/template2.tmpl}' 13 '${__tool_directory__}/templates/template2.tmpl}'
13 '${out_html}' 14 '${out_html}'
14 '${out_tab}' 15 '${out_tab}'
15 ]]> 16 ]]>
16 </command> 17 </command>
17 <inputs> 18 <inputs>
18 <param name="tabular_blast_report_input" type="data" format="tabular" label="Tabular BLAST results (extended 26 columns)"/> 19 <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="min_identity" 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="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 <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes">
22 <options from_data_table="blast_reference_bins"> 23 <options from_data_table="blast_reference_bins">
23 <validator type="no_options" message="No BLAST reference bins available" /> 24 <validator type="no_options" message="No BLAST reference bins available" />
24 </options> 25 </options>