Mercurial > repos > drosofff > msp_blastparser_and_hits
comparison BlastParser_and_hits.xml @ 16:0e51eef139ab draft default tip
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 |
| children |
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| 15:1991c830504a | 16:0e51eef139ab |
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| 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> |