annotate hexrd_find_orientations.xml @ 10:a35bda7ed678 draft default tip

"planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty"

<tool id="hexrd_find_orientations" name="HEXRD find-orientations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
    <description>Process rotation image series to find grain orientations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        cp '$config_yml' $config &&
        cp '$config_yml' config.yml &&
        ## symlink input files
        @CMD_LINKS@
        hexrd find-orientations --clean config.yml &&
        @CONVERT2TAB@ &&
        cp find-orientations_analysis_*.log '$log' &&
        cp  accepted_orientations_analysis_*.dat '$accepted_orientations' &&
        cp  scored_orientations_analysis_*.npz '$score_orientations' &&
        cp analysis_*_eta-ome_maps.npz '$ome_maps' 
    ]]></command>
    <configfiles>
        <configfile name="config_yml"><![CDATA[@FIND_ORIENTATIONS_YML@
]]></configfile>
    </configfiles>

    <inputs>
        <expand macro="find_orientations_config"/> 
    </inputs>
    <outputs>
        <data name="config" format="yaml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
        <data name="log" format="txt" label="${tool.name} on ${on_string}: find-orientations_analysis_${active_material}.log"/>
        <data name="ome_maps" format="hexrd.eta_ome.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/>
        <data name="score_orientations" format="hexrd.scored_orientations.npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
        <data name="accepted_orientations" format="hexrd.accepted_orientations" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
        <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
    </outputs>
    <tests>
        <!-- Test-1 single_GE -->
        <test>
            <param name="analysis_name" value="ruby"/>
            <param name="inputs" ftype="hexrd.images.npz" value="single_GE/RUBY_0000-fc_GE.npz,single_GE/RUBY_0001-fc_GE.npz,single_GE/RUBY_0002-fc_GE.npz,single_GE/RUBY_0003-fc_GE.npz,single_GE/RUBY_0004-fc_GE.npz,single_GE/RUBY_0005-fc_GE.npz"/>
            <conditional name="detector">
                <param name="panel_assignment" value="infer_from_name"/>
            </conditional>
            <param name="instrument" ftype="hexrd.yml" value="single_GE/ge_detector.yml"/>
            <param name="material" ftype="hexrd.materials.h5" value="single_GE/materials.h5"/>
            <param name="active_material" value="ruby"/>
            <param name="dmin" value="0.7"/>
            <param name="tth_width" value="0.2"/>
            <param name="min_sfac_ratio" value="0.05"/>
            <section name="orientation_maps">
                <param name="threshold" value="25"/>
                <param name="bin_frames" value="1"/>
                <param name="active_hkls" value="0,1,2,3,4,5"/>
            </section>
            <section name="search_options">
                <conditional name="search">
                    <param name="search_type" value="seed_search"/>
                    <param name="hkl_seeds" value="0,1,2"/>
                    <param name="fiber_step" value="0.5"/>
                    <conditional name="params">
                        <param name="method" value="label"/>
                        <param name="filter_radius" value="1"/>
                        <param name="threshold" value="1"/>
                    </conditional>
                </conditional>
            </section>
            <section name="omega">
                <param name="omega_tolerance" value="1.0"/>
            </section>
            <section name="eta">
                <param name="eta_tolerance" value="1.0"/>
                <param name="eta_mask" value="5.0"/>
            </section>
            <section name="clustering">
                <param name="clustering_algorithm" value="dbscan"/>
                <param name="clustering_radius" value="1.0"/>
                <param name="clustering_completeness" value="0.85"/>
            </section>
            <output name="grains">
                <assert_contents>
                    <has_text text="6.670" />
                </assert_contents>
            </output>
        </test>
        <!-- Test-2 multiruby_dexelas -->
        <test>
            <param name="analysis_name" value="ruby"/>
            <param name="inputs" ftype="hexrd.images.npz" value="multiruby_dexelas/mruby-0129_000004_ff1_000012-cachefile.npz,multiruby_dexelas/mruby-0129_000004_ff2_000012-cachefile.npz"/>
            <conditional name="detector">
                <param name="panel_assignment" value="infer_from_name"/>
            </conditional>
            <param name="instrument" ftype="hexrd.yml" value="multiruby_dexelas/dexelas_id3a_20200130.yml"/>
            <param name="material" ftype="hexrd.materials.h5" value="multiruby_dexelas/materials.h5"/>
            <param name="active_material" value="ruby"/>
            <param name="dmin" value="0.7"/>
            <param name="tth_width" value="0.2"/>
            <param name="min_sfac_ratio" value="0.05"/>
            <section name="orientation_maps">
                <param name="threshold" value="250"/>
                <param name="bin_frames" value="1"/>
                <param name="active_hkls" value="0,1,2,3,4,5"/>
            </section>
            <section name="search_options">
                <conditional name="search">
                    <param name="search_type" value="seed_search"/>
                    <param name="hkl_seeds" value="0,1,2"/>
                    <param name="fiber_step" value="0.5"/>
                    <conditional name="params">
                        <param name="method" value="blob_log"/>
                            <param name="min_sigma" value="0.5"/>
                            <param name="max_sigma" value="5.0"/>
                            <param name="num_sigma" value="10"/>
                            <param name="threshold" value="0.01"/>
                            <param name="overlap" value="0.1"/>
                    </conditional>
                </conditional>
            </section>
            <section name="omega">
                <param name="omega_tolerance" value="1.0"/>
            </section>
            <section name="eta">
                <param name="eta_tolerance" value="1.0"/>
                <param name="eta_mask" value="5.0"/>
            </section>
            <section name="clustering">
                <param name="clustering_algorithm" value="dbscan"/>
                <param name="clustering_radius" value="1.0"/>
                <param name="clustering_completeness" value="0.85"/>
            </section>
            <output name="grains">
                <assert_contents>
                    <has_text text="6.94" />
                </assert_contents>
            </output>
        </test>

    </tests>
    <help><![CDATA[
**HEXRD find-orientations**
@HEXRD_HELP@
@COMMON_INPUTS_HELP@
@FIND_ORIENTATIONS_OUTPUTS_HELP@
    ]]></help>
    <expand macro="citations" />
</tool>