Mercurial > repos > bornea > filter_fasta
view filter_fasta.xml @ 14:d66c62c6c56f draft
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author | bornea |
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date | Wed, 24 Aug 2016 13:00:03 -0400 |
parents | 55990dea42fb |
children | 3833aebf8d3a |
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<tool id="filter_fasta" name="Filter FASTA"> <description></description> <command interpreter="python">filter_fasta.py $fasta_input $scaf_input $fasta_output</command> <inputs> <param format="fasta" name="fasta_input" type="data" label="FASTA Database"/> <param format="txt" name="scaf_input" type="data" label="Scaffold Report"/> </inputs> <outputs> <data format="fasta" name="fasta_output" label="Filtered FASTA"/> </outputs> <stdio> <regex match="Error|error" source="stdout" level="fatal" description="Unknown error"/> <regex match="Error|error" source="stderr" level="fatal" description="Unknown error"/> <regex match="Error: bad bait" source="stdout" level="fatal" description="Error: bad bait"/> </stdio> <tests> <test> <param name="input" value="fa_gc_content_input.fa"/> <output name="out_file1" file="fa_gc_content_output.txt"/> </test> </tests> <help> This program will filter a fasta file using a data file containing an "Accession" or "Accession Number" column. **Required input:** 1) fasta file to be filtered 2) data file containing a "Accession" or "Accession Number" column </help> </tool>