view hal_halAddToBranch.xml @ 2:fb30a33c372a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit f46096b336bf460424143fc9d633b5e7c20bf1cf

<tool id="hal_haladdtobranch" name="halAddToBranch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>adds a new internal node and leaf genome into an existing HAL </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 && 
        halAddToBranch
            $noMarkAncestors
            writable_hal.hal '$botAlignmentFile' '$topAlignmentFile' '$parentName' '$insertName' '$childName' '$leafName' '$upperBranchLength' '$leafBranchLength' &&
        ## echo 'ok' to check it with assert_stdout. This is needed because there is no other stdout output, 
        ## and the output HAL file checksum always changes even with identical inputs.
        echo 'ok'
    ]]></command>
    <inputs>
        <expand macro="input_hal"/>
        <param name="insertName" type="text" value="" label="Insert name" help="Name of the new internal node to be created. Must be present in both top and bottom alignment files">
            <expand macro="sanitizer_default"/>
            <expand macro="validator_trim"/>
        </param>
        <param name="parentName" type="text" value="" label="Parent name" help="Name of the existing genome in the main tree that will become the parent of the new insert node">
            <expand macro="sanitizer_default"/>
            <expand macro="validator_trim"/>
        </param>
        <param name="childName" type="text" value="" label="Child name" help="Name of the existing genome that is being moved. It will be detached from the parent and re-attached to the new insert">
            <expand macro="sanitizer_default"/>
            <expand macro="validator_trim"/>
        </param>
        <param name="leafName" type="text" value="" label="Leaf name" help="Name of the new leaf genome being added to the tree. Must be present in the bottom alignment file">
            <expand macro="sanitizer_default"/>
            <expand macro="validator_trim"/>
        </param>
        <param name="topAlignmentFile" type="data" format="hal" label="Top alignment file" help="HAL file defining the connection between the parent and the new insert. A tree containing the insert, its parent, and its siblings"/>
        <param name="botAlignmentFile" type="data" format="hal" label="Bottom alignment file" help="HAL file defining the subtree starting from the new insert node. A tree containing the insert, its children, and its new leaf genome"/>
        <param name="upperBranchLength" type="float" value="1" min="0" label="Upper branch length" help="Length of branch from parent to insert"/>
        <param name="leafBranchLength" type="float" value="1" min="0" label="Leaf branch length" help="Leaf branch length"/>
        <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="botAlignmentFile" value="halAddToBranch_bot_input.hal"/>
            <param name="topAlignmentFile" value="halAddToBranch_top_input.hal"/>
            <param name="parentName" value="Genome_0"/>
            <param name="insertName" value="Insert"/>
            <param name="childName" value="Genome_2"/>
            <param name="leafName" value="NewLeaf"/>
            <param name="upperBranchLength" value="1"/>
            <param name="leafBranchLength" value="1"/>
            <output name="out_file" ftype="hal">
                <assert_contents>
                    <has_size min="80000"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_line line="ok"/>
            </assert_stdout>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="botAlignmentFile" value="halAddToBranch_bot_input.hal"/>
            <param name="topAlignmentFile" value="halAddToBranch_top_input.hal"/>
            <param name="parentName" value="Genome_0"/>
            <param name="insertName" value="Insert"/>
            <param name="childName" value="Genome_2"/>
            <param name="leafName" value="NewLeaf"/>
            <param name="upperBranchLength" value="1"/>
            <param name="leafBranchLength" value="1"/>
            <param name="noMarkAncestors" value="true"/>
            <output name="out_file" ftype="hal">
                <assert_contents>
                    <has_size min="80000"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_line line="ok"/>
            </assert_stdout>
        </test>
    </tests>
    <help><![CDATA[
halAddToBranch adds a new internal genome node and a new leaf genome to an input HAL alignment by splitting an existing branch. 
A new internal node is inserted between a specified parent and child, and a new leaf genome is attached to that inserted node.
Bottom and top alignment files are required to correctly connect the inserted node to its descendants and ancestors. 
By default, ancestor nodes are marked for update to ensure consistency of the alignment after replacement. 
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>