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comparison blast_report.xml @ 9:2b4f30c6b50a draft default tip

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planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report commit 174f746f44dfdeb18301429116ccc0213c1e091e-dirty
author dfornika
date Mon, 02 Mar 2020 23:41:54 +0000
parents 71dd0b1d5511
children
comparison
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8:71dd0b1d5511 9:2b4f30c6b50a
1 <tool id="blast_report" name="BLAST report" force_history_refresh="true" version="1.1.0"> 1 <tool id="blast_report" name="BLAST report" version="0.1.0+galaxy0" >
2 <description>Report on BLAST results</description> 2 <description>Produce an HTML table report of BLAST results</description>
3 <command > 3 <command detect_errors="error_code">
4 <![CDATA[ 4 <![CDATA[
5 '$__tool_directory__/blast_report.py' 5 '${__tool_directory__}/blast_report.py'
6 '${in_tab}' 6 '${tabular_blast_report_input}'
7 '${tmpl.fields.path}' 7 '${report_template}'
8 '${out_html}' 8 '${out_html}'
9 '${out_tab}' 9 '${out_tab}'
10 -f '${filter_pident}:$filter_kws' 10 -f ${filter_pident}:$filter_kws
11 #if str($bins) == "None" 11 #if str($bins) != "None"
12 #pass 12 -b "${bins}"
13 #else 13 #end if
14 -b "${bins.fields.path}" 14 $discard_redundant
15 #end if
16 #if $hsp_bool
17 -r
18 #end if
19 ]]> 15 ]]>
20 </command> 16 </command>
21 <inputs> 17 <inputs>
22 <param name="in_tab" type="data" format="tabular" label="Tabular BLAST results (extended 26 columns)"/> 18 <param name="tabular_blast_report_input" type="data" format="tabular" label="Tabular BLAST results (extended 26 columns)"/>
23 <param name="tmpl" type="select" optional="false" label="Report template"> 19 <param name="report_template" type="select" optional="false" label="Report template">
24 <options from_data_table="blast_report_templates"> 20 <options from_data_table="blast_report_templates">
25 <column name="value" index="0"/> 21 <validator type="no_options" message="No BLAST report templates are available" />
26 <column name="name" index="1"/>
27 <column name="path" index="2"/>
28 </options> 22 </options>
29 </param> 23 </param>
30 <param name="filter_pident" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/> 24 <param name="filter_pident" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
31 <param name="filter_kws" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/> 25 <param name="filter_kws" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
32 <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes"> 26 <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes">
33 <options from_data_table="blast_report_bins"> 27 <options from_data_table="blast_reference_bins">
34 <column name="value" index="0"/> 28 <validator type="no_options" message="No BLAST reference bins available" />
35 <column name="name" index="1"/>
36 <column name="path" index="2"/>
37 </options> 29 </options>
38 </param> 30 </param>
39 <!--<repeat name="hist_bins" title="History database bins"> 31 <param name="discard_redundant" type="boolean" truevalue="-r" falsevalue="" label="Throw out redundant hits?"/>
40 <param name="filter" type="data" format="csv" label="History database bin"/> 32 <param name="output_tabular" type="boolean" label="Output tabular file?"/>
41 </repeat>-->
42 <param name="hsp_bool" type="boolean" label="Throw out redundant hits?"/>
43 <param name="tab_bool" type="boolean" label="Output tabular file?"/>
44 </inputs> 33 </inputs>
45 <outputs> 34 <outputs>
46 <data name="out_html" format="html" label="$tool.name on data $in_tab.hid: report"/> 35 <data name="out_html" format="html" label="$tool.name on data $in_tab.hid: report"/>
47 <data name="out_tab" format="tabular" label="$tool.name on data $in_tab.hid: tabular results"> 36 <data name="out_tab" format="tabular" label="$tool.name on data $in_tab.hid: tabular results">
48 <filter> tab_bool </filter> 37 <filter> output_tabular </filter>
49 </data> 38 </data>
50 </outputs> 39 </outputs>
51 <help> 40 <help>
41
52 .. class:: infomark 42 .. class:: infomark
53 43
54 **What it does** 44 **What it does**
55 45
56 This tool produces a HTML report for each query in a tabular BLAST file. 46 This tool produces a HTML report for each query in a tabular BLAST file.