Mercurial > repos > devteam > megablast_xml_parser
comparison megablast_xml_parser.xml @ 1:3ce5d56297ed draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser commit 3ccddd4e2032535ead030efa401e690ffb80d145"
author | devteam |
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date | Wed, 09 Sep 2020 10:27:20 +0000 |
parents | 35ff246876fc |
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0:35ff246876fc | 1:3ce5d56297ed |
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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> |