comparison fasta_add_barcode.xml @ 0:8b37115e8d6b draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fasta_add_barcode commit d28e31b1b4dbcc3c406a4e8a5a41ac4576bf4f43-dirty

0:8b37115e8d6b

<tool id="fasta_add_barcode" name="Add barcodes">

    <description>to FASTA sequences</description>

    <requirements>
        <requirement type='package' version="1.0">fasta_add_barcode</requirement>
    </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_sequence_file"/>
            <param name="mapping_file" value="mapping_file"/>
            <param name="output_sequence_file" value="output_sequence_file" />
        </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 sequence identifier and the mapping 
file.

]]>
    </help>

    <citations>
    </citations>
</tool>