Mercurial > repos > sanbi-uwc > data_manager_novoalign_index_builder

<?xml version="1.0" encoding="utf-8" ?>
<tool id="novoalign_index_builder" name="NOVO ALIGN index" tool_type="manage_data" version="0.0.1">
    <description>Build an index for use by the Novo Align mapping tool</description>
    <stdio>
        <exit_code range=":-1" />
        <exit_code range="1:" />
    </stdio>
    <command interpreter="python">
        novoalign_index_builder.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() } --data_table_name "novocraft_index"
    </command>
    <inputs>
        <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
        <param type="text" name="sequence_name" value="" label="Name of sequence" />
        <param type="text" name="sequence_desc" value="" label="Description of sequence" />
        <param type="text" name="sequence_id" value="" label="ID for sequence" />
        <conditional name="reference_source">
          <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
            <option value="url">URL</option>
            <option value="history">History</option>
          </param>
          <when value="url">
            <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
          </when>
          <when value="history">
            <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
          </when>
        </conditional>
    </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	Fri, 04 Mar 2016 07:56:53 -0500
parents	e51fb8188ed9
children