view data_manager/novocraft_index_builder.xml @ 16:6437b3c7bb84 draft

planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit b51c474554b3c91ee75afaceb7b44d048eff0c15-dirty

<?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>
    <requirements>
        <requirement type="package" version="3.04.01">novocraft</requirement>
    </requirements>
    <stdio>
        <exit_code range=":-1" />
        <exit_code range="1:" />
    </stdio>
    <command interpreter="python">
        novocraft_index_builder.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() } --data_table_name "novocraft_index" --add_system_module ${add_system_module}
    </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>
        <param name="add_system_module" type="boolean" label="Add a Novo-align system Module" checked="true" truevalue="true" value="false" help="Add novoindex system module"/>
    </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>