view fasta_header_converter.xml @ 0:4f9e5110914b draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-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>