view fasta_header_converter.xml @ 3:dd268de3a107 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 988b1fc1cb8739e45648465adbf099f3fdaf87f8

<tool id="fasta_header_converter" name="FASTA header converter" version="0.1.1">
    <description>to append species information</description>
    <command detect_errors="exit_code">
<![CDATA[
python '$__tool_directory__/fasta_header_converter.py'
-f '$fastaFile'
-j '$genesFile'
-o '$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>