Mercurial > repos > devteam > megablast_xml_parser

comparison megablast_xml_parser.xml @ 1:fbff957a3655 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser commit 3ccddd4e2032535ead030efa401e690ffb80d145"
author devteam
date Wed, 09 Sep 2020 10:27:39 +0000
parents 03ca082aeb2e
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0:03ca082aeb2e 1:fbff957a3655
1 <tool id="megablast_xml_parser" name="Parse blast XML output" version="1.0.0"> 1 <tool id="megablast_xml_parser" name="Parse blast XML output" version="1.0.1">
2 <description></description> 2 <description></description>
3 <command interpreter="python">megablast_xml_parser.py $input1 $output1</command> 3 <requirements>
4 <inputs> 4 <requirement type="package" version="3.8">python</requirement>
5 <param name="input1" type="data" format="blastxml" label="Megablast XML output" /> 5 </requirements>
6 </inputs> 6 <command><![CDATA[
7 <outputs> 7 python '$__tool_directory__/megablast_xml_parser.py' '$input1' '$output1'
8 <data name="output1" format="tabular"/> 8 ]]></command>
9 </outputs> 9 <inputs>
10 <tests> 10 <param name="input1" type="data" format="blastxml" label="Megablast XML output" />
11 <test> 11 </inputs>
12 <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" /> 12 <outputs>
13 <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" /> 13 <data name="output1" format="tabular"/>
14 </test> 14 </outputs>
15 </tests> 15 <tests>
16 <test>
17 <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" />
18 <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" />
19 </test>
20 </tests>
16 <help> 21 <help>
17 22
18 **What it does** 23 **What it does**
19 24
20 This tool processes the XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option). 25 This tool processes the XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option).
52 57
53 .. class:: infomark 58 .. class:: infomark
54 59
55 Note that this form of output does not contain alignment identify value. However, it can be computed by dividing the number of identical bases within the alignment (Field 13) by the alignment length (Field 14) using *Text Manipulation->Compute* tool 60 Note that this form of output does not contain alignment identify value. However, it can be computed by dividing the number of identical bases within the alignment (Field 13) by the alignment length (Field 14) using *Text Manipulation->Compute* tool
56 61
57 62 </help>
58
59 </help>
60 </tool> 63 </tool>