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comparison BlastParser_and_hits.xml @ 16:0e51eef139ab draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit c81a2a37d69ad570068741411bae12dd8289d60c-dirty
author drosofff
date Wed, 11 Oct 2017 12:43:04 -0400
parents 1991c830504a
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15:1991c830504a 16:0e51eef139ab
1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.4.3"> 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.4.4">
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'
22 --dataset_name "$blast.element_identifier" 22 --dataset_name "$blast.element_identifier"
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>
29 </param>
28 <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"/>
29 <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">
30 <option value="verbose" selected="true">extensive</option> 32 <option value="verbose" selected="true">extensive</option>
31 <option value="short">compact</option> 33 <option value="short">compact</option>
32 </param> 34 </param>