annotate ogs_simulation.xml @ 0:ce3d848dff57 draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/ commit 8d522c2d14b28a4df096a5a13cd800bbf086f09f

<tool id="ogs_simulation" name="OGS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Runs an OGS simulation
    </description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <expand macro="ogs_requirement"/>
    </requirements> 
    <expand macro="creator"/>       
    <command detect_errors="exit_code"><![CDATA[  
        #import re 
        
        ln -s '$project_file' main_file.prj &&
        #for $f in $project_files:
           #set $identifier= re.sub(r'[^\w\-.]', '_', $f.element_identifier)
            ln -s '$f' '$identifier' &&
        #end for
        #for $file in $xml_patch_files:
            #set $identifier= re.sub(r'[^\w\-.]', '_', $file.element_identifier)
            ln -s '$file' '$identifier' &&
        #end for
        
        ogs main_file.prj
        #if $log_level: 
        --log-level '${log_level}' 
        #end if     
        
        #for $file in $xml_patch_files:
            #set $identifier= re.sub(r'[^\w\-.]', '_', $file.element_identifier)
            --xml-patch '$identifier' 
        #end for
       -o output
    ]]></command>
    <inputs>
        <param name="project_file" format="prj" type="data" label="Project File"/>
        <param name="project_files" format="data" type="data_collection" collection_type="list" label="Project Files"/>
        <param name="xml_patch_files" format="xml" type="data_collection" collection_type="list" label="XML Patch Files"/>
        <param name="log_level" type="select" label="Log Level" optional="true">
            <option value="none">None</option>
            <option value="error">Error</option>
            <option value="warn">Warning</option>
            <option value="info" selected="true">Info</option>
            <option value="debug">Debug</option>
            <option value="all">All</option>
        </param>
    </inputs>
    <outputs>
        <collection name="simulation_results" type="list">
            <discover_datasets pattern="(?P&lt;designation&gt;.*\.pvd)" directory="output" visible="true"/>
            <discover_datasets pattern="(?P&lt;designation&gt;.*\.vtu)" format="vtkxml" directory="output" visible="true"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="project_file" value="square_1e0_neumann.prj" />
            <param name="project_files">
                <collection type="list">
                    <element name="square_1x1_quad_1e0.vtu" value="square_1x1_quad_1e0.vtu"/>
                    <element name="square_1x1.gml" value="square_1x1.gml"/>
                </collection>
            </param>
            <param name="xml_patch_files">
                <collection type="list">
                    <element name="square_1e0.xml" value="square_1e0.xml" ftype="xml"/>
                    <element name="square_neumann.xml" value="square_neumann.xml" ftype="xml"/>
                </collection>
            </param>
            <param name="log_level" value="info" />
            <output_collection name="simulation_results" type="list" count="3">
                <element name="square_1e0_neumann_neumann.pvd">
                    <assert_contents>
                        <has_text text="VTKFile type=&quot;Collection&quot;" />
                        <has_n_lines min="5" max="7"/>
                    </assert_contents>
                </element>
                <element name="square_1e0_neumann_neumann_ts_0_t_0.000000.vtu">
                    <assert_contents>
                        <has_text text="VTKFile type=&quot;UnstructuredGrid&quot;" />
                        <has_n_lines min="23" max="27"/>
                    </assert_contents>
                </element>
                <element name="square_1e0_neumann_neumann_ts_1_t_1.000000.vtu">
                    <assert_contents>
                        <has_text text="VTKFile type=&quot;UnstructuredGrid&quot;"/>
                        <has_n_lines min="23" max="27"/>
                    </assert_contents>
                </element>
                
           </output_collection>
        </test>
    </tests>

    <help><![CDATA[
        **Overview:**

            This tool runs an OpenGeoSys (OGS) simulation with support for Python boundary conditions and enhanced CLI argument parsing. The simulation uses a project file and optional XML patch files to define and adjust simulation parameters dynamically.

        **Inputs:**

            1. **Project File:** The main project file (.prj) that defines the simulation setup.
            2. **Project Files:** The files mentioned in the Project File (.prj).
            3. **XML Patch Files:** Optional XML files for modifying the project file configuration at runtime.
            4. **Log Level:** Sets the verbosity of logs. Options include `none`, `error`, `warn`, `info` (default), `debug`, and `all`.
           
        **Outputs:**

            1. **Log File:** Contains all log messages generated during the simulation.
            2. **Simulation Results:** Includes output files such as VTU and other simulation results saved in the specified output directory.
    ]]></help>
    <expand macro="ogs_citation"/>
</tool>