comparison fasta_add_barcode.xml @ 0:04699558a38a draft default tip

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fasta_add_barcode commit e857f7126443e115f11954085423f8999bc870aa-dirty

0:04699558a38a

<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>