Mercurial > repos > drosofff > msp_blastparser_and_hits

comparison BlastParser_and_hits.xml @ 4:60b6bd959929 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
author drosofff
date Fri, 15 Jan 2016 12:29:30 -0500
parents 8f5d48294f70
children 78c34df2dd8d
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3:8f5d48294f70 4:60b6bd959929
1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.2"> 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.3">
2 <description>for virus discovery</description> 2 <description>for virus discovery</description>
3 <requirements></requirements> 3 <requirements></requirements>
4 <command interpreter="python"> 4 <command interpreter="python">
5 BlastParser_and_hits.py 5 BlastParser_and_hits.py
6 --sequences $sequences 6 --sequences $sequences
12 ## Additional parameters. 12 ## Additional parameters.
13 #if $additional_filters.use_filters == "yes": 13 #if $additional_filters.use_filters == "yes":
14 --filter_relativeCov $additional_filters.filter_relativeCov 14 --filter_relativeCov $additional_filters.filter_relativeCov
15 --filter_maxScore $additional_filters.filter_maxScore 15 --filter_maxScore $additional_filters.filter_maxScore
16 --filter_meanScore $additional_filters.filter_meanScore 16 --filter_meanScore $additional_filters.filter_meanScore
17 --filter_term_in "$additional_filters.filter_term_in"
18 --filter_term_out "$additional_filters.filter_term_out"
17 #end if 19 #end if
18 --al_sequences $al_sequences 20 --al_sequences $al_sequences
19 --un_sequences $un_sequences 21 --un_sequences $un_sequences
20 22
21 </command> 23 </command>
36 </when> 38 </when>
37 <when value="yes"> 39 <when value="yes">
38 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/> 40 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
39 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/> 41 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
40 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/> 42 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
43 <param name="filter_term_in" type="text" value="" label="filter the subject list with a keyword" help=""/>
44 <param name="filter_term_out" type="text" value="" label="filter the subject list excluding a keyword" help=""/>
41 </when> 45 </when>
42 </conditional> 46 </conditional>
43 </inputs> 47 </inputs>
44 <outputs> 48 <outputs>
45 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/> 49 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>