view hedm_npz_to_tesr.xml @ 4:b49a8ef3351d draft

"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"

<tool id="hedm_npz_to_tesr" name="HEDM to tesr" version="0.1.0" python_template_version="3.5">
    <description>Convert HEDM npz to a Neper tesr</description>
    <requirements>
        <requirement type="package" version="1.19">numpy</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        $__tool_directory__/hedm_npz_to_tesr.py 
        --voxel_spacing $voxel_spacing 
        #if $names.x_name:
            -x '$names.x_name'
        #end if 
        #if $names.y_name:
            -y '$names.y_name'
        #end if 
        #if $names.z_name:
            -z '$names.z_name'
        #end if 
        #if $names.grain_map:
            --grain_map '$names.grain_map'
        #end if 
        '$input' 
        '$output'
    ]]></command>
    <inputs>
        <!-- change format to approriate npz subclass when available -->
        <param name="input" type="data" format="zip" label="HEDM npz file"/>
        <param name="voxel_spacing" type="float" value="0.005" min="0" label="Voxel spacing"/>
        <section name="names" expanded="false" title="Specify names used in HEDM.npz input file">
            <param name="x_name" type="text" value="" label="Name of the X array in the input" optional="true" help="Deafault is a name containing 'X'"/>
            <param name="y_name" type="text" value="" label="Name of the Y array in the input" optional="true" help="Deafault is a name containing 'Y'"/>
            <param name="z_name" type="text" value="" label="Name of the Z array in the input" optional="true" help="Deafault is a name containing 'Z'"/>
            <param name="grain_map" type="text" value="" label="Name of the grain map in the input" optional="true" help="Deafault is a name containing 'grain'"/>
	</section>
    </inputs>
    <outputs>
        <!-- output format should be changed to tesr when that is available -->
        <data name="output" format="txt" label="${input.name.rsplit(sep='.',maxsplit=1)[0]}.tesr"/>
    </outputs>
    <tests>
        <test>
            <!-- change format to approriate npz subclass when available -->
            <param name="input" ftype="zip" value="HEDM_map.npz"/>
            <output name="output" file="HEDM_map.tesr"/> 
        </test>
    </tests>
    <help><![CDATA[
        Create a neper compatible tesr format file from a HEDM numpy compressed file.  
        The converter will look for columns named: Xs, Ys, Zs, and grain_map by default,
        If the input file uses different names, the user should specify them.
    ]]></help>
</tool>