view fasta_header_converter.xml @ 2:7ea4df039a53 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 978a8efb9969646b97873d69348971860f2793f5

<tool id="fasta_header_converter" name="FASTA header converter" version="0.1.1">
    <description>to append species information</description>
    <command>
<![CDATA[
python '$__tool_directory__/fasta_header_converter.py'
-f '$fastaFile'
-j '$genesFile'
> '$outputFile'
]]>
    </command>
    <inputs>
        <param name="fastaFile" type="data" format="fasta" label="FASTA file" help="FASTA file with transcript ID as FASTA ID" />
        <param name="genesFile" type="data" format="json" label="Gene feature information" help="In JSON format" />
    </inputs>
    <outputs>
        <data format="fasta" name="outputFile" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="fastaFile" ftype="nhx" value="test.fasta" />
            <param name="genesFile" ftype="json" value="test.json" />
            <output name="outputFile" file="out.fasta" />
        </test>
    </tests>
    <help>
    <![CDATA[
Simple converter for FASTA files, which appends the species name to the FASTA header for usage in TreeBeST. It uses gene feature information in JSON format (similar to the result of Ensembl REST API - lookup/id).
    ]]>
    </help>
    <citations>
    </citations>
</tool>