Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder

<?xml version="1.0" encoding="utf-8" ?>
<tool id="novocraft_index_builder" name="NOVO CRAFT index" tool_type="manage_data" version="0.0.1">
    <description>Build an index for use by the Novo Craft mapping tool</description>
    <stdio>
        <exit_code range=":-1" />
        <exit_code range="1:" />
    </stdio>
    <requirements>
        <requirement type="package" version="1.2">samtools</requirement>
        <requirement type="package" version="3.04.01">novocraft</requirement>
    </requirements>
    <command interpreter="python">
        novocraft_index_builder.py "${out_file}" --input_filename "${input_fasta.fields.path}" --data_table_name "novocraft_index"
    </command>
    <inputs>
        <param type="text" name="sequence_name" value="" label="Name of sequence" optional="False" />
        <param type="text" name="sequence_desc" value="" label="Description of sequence" />
        <param type="text" name="sequence_id" value="" label="ID for sequence" optional="False" />
        <param name="input_fasta" type="select" label="Genome to index(FASTA format)">
            <options from_data_table="all_fasta"/>
        </param>

    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <param name="reference_source_selector" value="history"/>
            <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/>
        </test>
    </tests>
    <help>Help!</help>
    <citations>
        <citation></citation>
    </citations>
</tool>
author	sanbi-uwc
date	Tue, 21 Jun 2016 10:12:02 -0400
parents	db293ee25be5
children