Mercurial > repos > artbio > blastparser_and_hits

comparison BlastParser_and_hits.xml @ 1:9beb85dba280 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
author artbio
date Fri, 16 Feb 2018 04:54:52 -0500
parents 9dfb65ebb02e
children 36103afa0934
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0:9dfb65ebb02e 1:9beb85dba280
1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.5.0"> 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.5.1">
2 <description>for virus discovery</description> 2 <description>for virus discovery</description>
3 <requirements></requirements> 3 <requirements></requirements>
4 <command><![CDATA[ 4 <command><![CDATA[
5 python '$__tool_directory__'/BlastParser_and_hits.py 5 python '$__tool_directory__'/BlastParser_and_hits.py
6 --sequences '$sequences' 6 --sequences '$sequences'
23 23
24 ]]></command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" /> 26 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" />
27 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse"> 27 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse">
28 <validator type="expression" message="Blast file must have 13 columns">value.metadata.columns == 13</validator> 28 <validator type="expression" message="Blast file must have 13 columns">value.metadata.columns == 13 or value.metadata.columns == 0</validator>
29 </param> 29 </param>
30 <param name="flanking" type="integer" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/> 30 <param name="flanking" type="integer" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
31 <param name="mode" type="select" label="Extensive or compact reporting mode" help="display (extensive) or not (compact) the oases contigs"> 31 <param name="mode" type="select" label="Extensive or compact reporting mode" help="display (extensive) or not (compact) the oases contigs">
32 <option value="verbose" selected="true">extensive</option> 32 <option value="verbose" selected="true">extensive</option>
33 <option value="short">compact</option> 33 <option value="short">compact</option>
37 <option value="no">No</option> 37 <option value="no">No</option>
38 <option value="yes">Yes</option> 38 <option value="yes">Yes</option>
39 </param> 39 </param>
40 <when value="no"> 40 <when value="no">
41 </when> 41 </when>
42 <when value="yes"> 42 <when value="yes">
43 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/> 43 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
44 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/> 44 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
45 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/> 45 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
46 <param name="filter_term_in" type="text" value="" label="filter the subject list with a keyword" help=""/> 46 <param name="filter_term_in" type="text" value="" label="filter the subject list with a keyword" help=""/>
47 <param name="filter_term_out" type="text" value="" label="filter the subject list excluding a keyword" help=""/> 47 <param name="filter_term_out" type="text" value="" label="filter the subject list excluding a keyword" help=""/>