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author | bebatut |
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date | Fri, 15 Apr 2016 06:04:56 -0400 |
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<tool id="fasta_add_barcode" name="Add barcodes" version="1.0"> <description>to FASTA sequences</description> <requirements> </requirements> <stdio> </stdio> <version_command>python -version</version_command> <!--<command>--> <command><![CDATA[ python $__tool_directory__/fasta_add_barcode.py --input_sequence_file $sequence_file --input_mapping_file $mapping_file --output_sequence_file $output_sequence_file ]]> </command> <inputs> <param name="sequence_file" type="data" format="fasta" label="Sequence zfile" help=""/> <param name="mapping_file" type="data" format="tabular" label="Mapping file between sequence identifier and barcode to add" help="The mapping file must be a tabular delimited file with two columns. The first column contains sequence identifier and the second column corresponding barcode to add at the beginning of each sequence."/> </inputs> <outputs> <data format="fasta" name="output_sequence_file" metadata_source="sequence_file" label="Sequences with added barcodes from ${on_string}" /> </outputs> <tests> <test> <param name="sequence_file" value="input_sequences.fasta"/> <param name="mapping_file" value="mapping_file.txt"/> <output name="output_sequence_file" file="output_test.fasta" /> </test> </tests> <help><![CDATA[ **What it does** This tool takes a FASTA file and add at the beginning of each sequence a barcode. The barcode of each sequence is determined given its sequence identifier. The mapping between sequence identifier and corresponding barcode is defined inside the mapping file. This file must be a tabular delimited file with two columns: the first with sequence identifiers and the second the corresponding barcode. ]]> </help> <citations> </citations> </tool>