<tool id="hal_halremovesubtree" name="halRemoveSubtree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>removes an entire subtree in a HAL file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/> 
    <expand macro="stdio"/>
    <command detect_errors="aggressive"><![CDATA[
        ## Copy input HAL to ensure that it is not modified.
        cp '$input_hal' writable_hal.hal && 
        halRemoveSubtree
            $noMarkAncestors
            writable_hal.hal '$root'
    ]]></command>
    <inputs>
        <expand macro="input_hal"/>
        <param name="root" type="text" value="" label="Node name" help="Subtree below this node will be deleted (but not the node itself). If a leaf genome is given, nothing happens">
            <expand macro="sanitizer_default"/>
            <expand macro="validator_trim"/>
        </param>
        <expand macro="params_noMarkAncestors"/>
    </inputs>
    <outputs>
        <data name="out_file" format="hal" label="${tool.name} on ${on_string}" from_work_dir="writable_hal.hal"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="root" value="Genome_0"/>
            <output name="out_file" ftype="hal">
                <assert_contents>
                    <has_size min="45000"/>
                </assert_contents>
            </output>
            <assert_stderr>
                <has_line line="[halRemoveSubtree] removing Genome_1"/>
            </assert_stderr>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="root" value="Genome_1"/>
            <output name="out_file" ftype="hal">
                <assert_contents>
                    <has_size min="50000"/>
                </assert_contents>
            </output>
            <assert_stderr>
                <has_line line="[halRemoveSubtree] Warning: given root Genome_1 is a leaf: doing nothing"/>
            </assert_stderr>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="root" value="Genome_0"/>
            <param name="noMarkAncestors" value="true"/>
            <output name="out_file" ftype="hal">
                <assert_contents>
                    <has_size min="45000"/>
                </assert_contents>
            </output>
            <assert_stderr>
                <has_line line="[halRemoveSubtree] removing Genome_1"/>
            </assert_stderr>
        </test>
    </tests>
    <help><![CDATA[
halRemoveSubtree removes all descendant genomes below a given node from an input HAL file and updates the tree structure accordingly. 
The given node itself is not removed. 
By default, ancestor nodes are marked for update to ensure consistency of the alignment after removal. 
This behavior can be disabled when ancestor updates are not required.

A new HAL file is created as output instead of modifying the input HAL file.

-----

.. class:: warningmark

Running the tool on a HAL file in mmap format will fail because this format type is not supported by this tool.
It is recommended to convert the input to HDF5 format first using halExtract.
    ]]></help>
    <expand macro="citation"/>
    <expand macro="creator"/>
</tool>