Ogs auto wrap#130
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bernt-matthias
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The macros files and the tool files need to be in the same directory.
Ultimately the tools should be generated in the ogs dir, or?
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Some more comments. Would be nice if you could check with planemo lint / serve if the tools are correct.
| <param name="node_array" type="boolean" label="node array" help="Assigns raster data to node array (default)" checked="false" truevalue="--node-array" falsevalue=""/> | ||
| <param name="scalar_name" type="text" optional="false" label="scalar name" help="The name of the newly created scalar array."/> | ||
| <param name="raster" type="data" optional="false" label="raster" help="Name of the input raster file " format="asc" multiple="false"/> | ||
| <param name="input" type="data" optional="false" label="input" help="Name of the input mesh file, " format="vtu" multiple="false"/> |
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There is no vtu datattype. Also many of the other data types are not yet in Galaxy. We should discuss a mapping / implementing them in Galaxy.
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- Create
.shed.yml. - removce saqc changes from this PR
…o the agreed description syntax
| </inputs> | ||
| <outputs> | ||
| <collection name="tool_outputs" type="list" label="Outputs from AddElementQuality"> | ||
| <discover_datasets pattern="output_.+\..+" format="auto" visible="true"/> |
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pattern does not work like this. you find some examples here: https://planemo.readthedocs.io/en/latest/writing_advanced.html#examples
the easiest would be if __designation_and_ext__ would work (requires that ogs extensions match the Galaxy datatype names .. which we might achieve with a bit of file renaming?)
| </collection> | ||
| </outputs> | ||
| <tests> | ||
| <expand macro="ogsutilssuite_tests"/> |
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You probably only want to include the tests for this tool, i.e. you need one macro per tool (but they can and should be in the same folder).
| <param name="nodata" type="float" value="false" optional="false" label="nodata" help="The no data value used for missing values, " min="0"/> | ||
| <param name="cell_array" type="boolean" label="cell array" help="Assigns raster data to cell array" checked="false" truevalue="--cell-array" falsevalue=""/> | ||
| <param name="node_array" type="boolean" label="node array" help="Assigns raster data to node array (default)" checked="false" truevalue="--node-array" falsevalue=""/> | ||
| <param name="scalar_name" type="text" optional="false" label="scalar name" help="The name of the newly created scalar array."/> |
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optional has no meaning for text parameters. Should be removed. Add a no_value validator instead.
| <inputs> | ||
| <param name="shape_file" type="data" optional="false" label="shape file" help="the name of the input shape " format="shp" multiple="false"/> | ||
| </inputs> | ||
| <outputs/> |
| #for $f in $input: | ||
| --input '$f' | ||
| #end for | ||
| #for $f in $json_file: |
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for loop needed (actually wrong) if multiple = false
| #end for | ||
| --output output_1.vtp]]></command> | ||
| <inputs> | ||
| <param name="gamma" type="float" value="smaller or larger values indicate a logarithmic or " "exponential increase" optional="false" label="gamma" help="Exponental increase coefficient. A value of "/> |
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Was ist " " im original?
| ) | ||
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| # --- CONFIGURATION --- | ||
| OGS_REPO_PATH = Path("/home/stehling/gitProjects/ogs") |
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Waere schoen, wenn das ein command line parameter sein koennte.
| return re.sub(r'[^a-zA-Z0-9_]+', '_', name) | ||
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| def discover_tools() -> List[Dict[str, Any]]: | ||
| """Scans the OGS repo and finds tools using multiple regex patterns.""" |
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Vlt noch etwas mehr docs. Die Funktion sucht ja auch schon alle parameter raus, oder?
| "-1*std::numeric_limits<double>::max()": "-1.7976931348623157E+308", | ||
| "-1 * std::numeric_limits<double>::max()": "-1.7976931348623157E+308", |
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Statt eines extra eintrags fuer -1*... und -1 * ... koennte man auch etwas robuster mit regexp ersetzen?
| full_arg_text = ' '.join(full_arg_text.replace('"', '').replace('\\n', ' ').split()) | ||
| full_arg_text_lower = full_arg_text.lower() | ||
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| if not long_flag: |
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was sing diese long_flag? also was wird hier geskipped?
…, filtering broken tools, pvd and file list inputs
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Merge into ogs folder
| --output_raster output_1.asc | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="scaling_value" type="float" optional="true" label="scaling value" help="value the function sin(x pi) sin(y pi) will be scaled with" /> |
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scaling_value has a default.
| @@ -0,0 +1,45 @@ | |||
| <?xml version="1.0" encoding="UTF-8"?> | |||
| @@ -0,0 +1,45 @@ | |||
| <?xml version="1.0" encoding="UTF-8"?> | |||
| <tool name="OGS: addDataToRaster" id="ogs_adddatatoraster" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> | |||
| <description>Galaxy wrapper for the OGS utility 'addDataToRaster'.</description> | |||
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Description does not help. Remove
also fixes that master was used in the gitlab access
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Automatic extraction of information and xml galaxy wrap creation for OGS tools.