view fasta_header_converter.xml @ 1:fd85bf67c4bb draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 6a1dfb73f2172182096724ce3bee400287fd9c2f-dirty

<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>