<tool id="hal_halextract" name="halExtract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>can be used to copy between formats</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/> 
    <expand macro="stdio"/>
    <command detect_errors="aggressive"><![CDATA[
        halExtract
            #if $root:
                --root '$root'
            #end if
            #if $outputFormat.type == 'mmap':
                --outputFormat 'mmap'
                --mmapFileSize $outputFormat.mmapFileSize
            #else if $outputFormat.type == 'hdf5':
                --outputFormat 'hdf5'
            #end if
            '$input_hal' '$output_file'
    ]]></command>
    <inputs>
        <expand macro="input_hal"/>
        <expand macro="params_root_optional"/>
        <conditional name="outputFormat">
            <param name="type" type="select" label="Output storage format">
                <!-- 
                At the moment, creating a HAL file in mmap format is disabled. The creation in HDF5 format is enforced.
                <option value="Same as input" selected="true">Same as input file</option> 
                <option value="mmap">mmap</option> 
                -->
                <option value="hdf5" selected="true">HDF5</option>
            </param>
            <when value="hdf5"/>
            <!-- 
            <when value="Same as input"/>
            <when value="mmap">
                <expand macro="params_mmap_size"/>
            </when> 
            -->
        </conditional>
    </inputs>
    <outputs>
        <data name="output_file" format="hal" label="${tool.name} on ${on_string}: ${outputFormat.type}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <output name="output_file" ftype="hal">
                <assert_contents>
                    <has_size min="50000"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="Extracting Genome_0"/>
            </assert_stdout>
        </test>
        <!-- 
        Disabled until mmap HAL format is allowed
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <conditional name="outputFormat">
                <param name="type" value="mmap"/>
                <param name="mmapFileSize" value="1"/>
            </conditional>
            <assert_stdout>
                <has_text text="Extracting Genome_0"/>
            </assert_stdout>
        </test>
        -->
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="root" value="Genome_1"/>
            <output name="output_file" ftype="hal">
                <assert_contents>
                    <has_size min="20000"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="Extracting Genome_1"/>
            </assert_stdout>
        </test>
    </tests>
    <help><![CDATA[
halExtract copies HAL files between different storage formats, such as HDF5 and mmap. 
It reads an input HAL file and writes an output HAL file in the desired format, optionally extracting a subtree rooted at a specified genome. 

- **HDF5** is standard container format for larger data sets with good compression characteristics.  
- The **mmap** format stores the raw data structures in a file, which is accessed by mapping it in memory using the mmap system call. HAL files in the mmap format are considerably bigger but often much faster to access. 
    
-----

.. class:: warningmark

At the moment, extraction to mmap format is disabled. The extraction to HDF5 format is enforced.    
    ]]></help>
    <expand macro="citation"/>
    <expand macro="creator"/>
</tool>