Mercurial > repos > dfornika > blast_report_basic

comparison blast_report_basic.xml @ 13:456b2b3d4094 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dfornika
date Tue, 03 Mar 2020 07:18:47 +0000
parents 6650fe4db541
children c86c3e33a34d
comparison
equal deleted inserted replaced
12:9cf35f30bfb4 13:456b2b3d4094
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 --min-identity ${min_identity} 6 --min-identity ${min_identity}
7 --filter-keywords '${filter_kws}' 7 --filter-keywords '${filter_keywords}'
8 #if str($bins) != "None" 8 #if str($bins) != "None"
9 -b '${bins}' 9 -b '${bins}'
10 #end if 10 #end if
11 $discard_redundant 11 $discard_redundant
12 '${tabular_blast_report_input}' 12 '${tabular_blast_report_input}'
13 '${__tool_directory__}/templates/template2.tmpl' 13 '${__tool_directory__}/templates/template2.tmpl'
14 '${out_html}' 14 '${out_html}'
15 '${out_tab}' 15 '${out_tab}'
16 ]]> 16 ]]>
17 </command> 17 </command>
18 <inputs> 18 <inputs>
19 <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 25 columns + qcov)"/>
20 <param name="min_identity" 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"/>
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="filter_keywords" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
22 <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes"> 22 <param name="bins" type="select" label="Reference Database Bins" multiple="true" display="checkboxes">
23 <options from_data_table="blast_reference_bins"> 23 <options from_data_table="blast_report_reference_database_bins">
24 <validator type="no_options" message="No BLAST reference bins available" /> 24 <validator type="no_options" message="No BLAST reference bins available" />
25 </options> 25 </options>
26 </param> 26 </param>
27 <param name="discard_redundant" type="boolean" truevalue="-r" falsevalue="" label="Throw out redundant hits?"/> 27 <param name="discard_redundant" type="boolean" truevalue="-r" falsevalue="" label="Throw out redundant hits?"/>
28 </inputs> 28 </inputs>