view data_manager/novoalign_index_builder.xml @ 0:85fbd52dbb36 draft

planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf

<?xml version="1.0" encoding="utf-8" ?>
<tool id="novoalign_index_builder" name="NOVO ALIGN index" version="0.0.1">
    <description>Build an index for use by the Novo Align mapping tool</description>
    <requirements>
        <requirement type="package" version="0.0.1d">novoalign</requirement>
    </requirements>
    <stdio>
        <exit_code range=":-1" />
        <exit_code range="1:" />
    </stdio>
    <command interpreter="python">
        novoalign_index_builder.py "${out_file}" --data_table_name "novo_index"
    </command>
    <inputs>
        <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>
            <option value="directory">Directory on Server</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>
          <when value="directory">
            <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
            <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
          </when>
        </conditional>
        <!-- <param type="text" name="sequence_name" value="" label="Name of sequence" />
        <param type="text" name="sequence_id" value="" label="ID for sequence" /> -->
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <param name="dbkey" value="anoGam1"/>
            <param name="sequence_name" value=""/>
            <param name="sequence_id" value=""/>
            <param name="reference_source_selector" value="history"/>
            <param name="input_fasta" value="phiX174.fasta"/>
            <param name="sort_selector" value="as_is"/>
            <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/>
        </test>
    </tests>
    <help>Help!</help>
    <citations>
        <citation></citation>
    </citations>
</tool>