<tool id="create_streamlines" name="Create streamlines" version="0.13.0">
    <description>within brain images</description>
    <requirements>
        <requirement type="package" version="0.13.0">dipy</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/create_streamlines.py'
--output_trackvis_header '$output_trackvis_header'
--output_superiorfrontal_nifti '$output_superiorfrontal_nifti'
--output_connectivity '$output_connectivity'
--output_corpuscallosum_sagittal '$output_corpuscallosum_sagittal'
--output_corpuscallosum_axial 'output_corpuscallosum_axial'
    ]]></command>
    <inputs>
        <param name="drmi_dataset" type="select" label="dRMI dataset">
            <option value="stanford_t1" selected="true">stanford_t1</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_corpuscallosum_axial" format="png" label="${tool.name}: Corpuscallosum Axial" />
        <data name="output_corpuscallosum_sagittal" format="png" label="${tool.name}: Corpuscallosum Sagittal" />
        <data name="output_connectivity" format="png" label="${tool.name}: Connectivity" />
        <data name="output_superiorfrontal_nifti" format="nifti1" label="${tool.name}: Superiorfrontal" />
        <data name="output_trackvis_header" format="txt" label="${tool.name}: Superiorfrontal Track Visualization Header" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
**What it does**

Uses the target function to target streamlines that either pass through or do
not pass through some region of the brain, the connectivity_matrix groups function
to count streamlines based on where in the brain they begin and end and the density
map function to count the number of streamlines that pass though every voxel of some image.

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**Options**

    </help>
    <citations>
    </citations>
</tool>