adding gem_tools

tools/gem_tools/.shed.yml

@@ -0,0 +1,25 @@
+name: gem_tools
+owner: iuc
+categories:
+  - Metabolomics
+  - Systems Biology
+  - Synthetic Biology
+description: "Tools for analyzing genome-scale metabolic models (GEMs) using COBRApy and related libraries."
+long_description: |
+  This repository contains a collection of Galaxy tools for performing various analyses on genome-scale
+  metabolic models (GEMs). The tools leverage COBRApy and other Python libraries to provide functionalities
+  such as phenotype phase plane analysis, gene knockout analysis, flux variability analysis, and more.
+homepage_url: https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology
+remote_repository_url: https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology
+type: unrestricted
+license: GNU GENERAL PUBLIC LICENSE
+auto_tool_repositories:
+  name_template: "{{ tool_id  }}"
+  description_template: "Wrapper for the gem_tools tool suite: {{ tool_name  }}"
+suite:
+  name: "suite_gem_tools"
+  description: "A suite of tools for analyzing genome-scale metabolic models (GEMs) using COBRApy and related libraries."
+  long_description: |
+      This repository contains a collection of Galaxy tools for performing various analyses on genome-scale metabolic models (GEMs).
+      The tools leverage COBRApy and other Python libraries to provide functionalities such as phenotype phase plane analysis, gene
+      knockout analysis, flux variability analysis, and more.

tools/gem_tools/gem_check_memote.xml

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+<tool id="gem_check_memote" name="Make GEM quality report" version="@VERSION@" profile="@PROFILE@">
+    <description>
+        using memote
+    </description>
+    <macros>
+        <import>gem_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command_memote"/>
+    <command>
+        memote report snapshot
+            '${cb_model_location}'
+            --filename '${output}'
+    </command>
+    <inputs>
+        <expand macro="input_model"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="html" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <!-- Test 1: Valid E. coli core model -->
+        <test>
+            <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Stoichiometric Consistency"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 2: Invalid model format -->
+        <test expect_failure="true">
+            <param name="cb_model_location" value="invalid_format.txt"/>
+            <assert_stderr>
+                <has_text text="Most likely the SBML model is not valid"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Memote Model Quality Check
+
+        The GEM Check Memote tool runs the Memote test suite to generate a detailed report on the quality of a genome-scale metabolic model (GEM). Memote assesses various model characteristics such as stoichiometric consistency and model annotations.
+
+        Inputs
+
+        `Model to check with memote`: The metabolic model in SBML format (.xml or .sbml) to be analyzed by Memote. Ensure the file conforms to SBML standards.
+
+        Outputs
+
+        `Memote report`: An HTML file that contains the full results of the Memote assessment. This report includes overall model quality scores and highlights any issues that need correction.
+
+        Usage Example
+
+        1. Upload your SBML model file.
+        2. Run the tool to generate the Memote report.
+        3. Review the report to identify any errors or areas for improvement in the model.
+
+        Troubleshooting
+
+        If the tool fails to run, ensure that your input file is a valid SBML model. Incorrect file formats or non-compliant models may trigger errors.
+
+        References
+
+        Full documentation and further examples can be found at: https://doi.org/10.1038/s41587-020-0446-y
+    ]]></help>
+    <citations>
+        <expand macro="citation_memote"/>
+    </citations>
+</tool>

tools/gem_tools/gem_escher_visualization.py

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+import argparse
+
+import cobra
+import pandas as pd
+from escher import Builder
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        prog="EscherVisualization",
+        description="This program visualizes an Escher map",
+        epilog="Adding an epilog, but doubt it's needed.",
+    )
+    parser.add_argument(
+        "-m",
+        "--cb_model_location",
+        dest="cb_model_location",
+        action="store",
+        type=str,
+        default=None,
+        required=False,
+        help="The model to use."
+    )
+    parser.add_argument(
+        "-f",
+        "--flux_distribution_location",
+        dest="flux_distribution_location",
+        action="store",
+        type=str,
+        default=None,
+        required=False,
+        help="The flux distribution to visualize."
+    )
+    parser.add_argument(
+        "-e",
+        "--expect_map",
+        dest="expect_map",
+        action="store",
+        type=str,
+        default=None,
+        required=True,
+        help="Is a map expected to be uploaded?"
+    )
+    parser.add_argument(
+        "-l",
+        "--model_to_download",
+        dest="model_to_download",
+        action="store",
+        type=str,
+        default=None,
+        required=False,
+        help="The model to download."
+    )
+    parser.add_argument(
+        "--map_load_name",
+        dest="map_load_name",
+        action="store",
+        type=str,
+        default=None,
+        required=False,
+        help="The name of the map to use."
+    )
+    parser.add_argument(
+        "--map_upload_name",
+        dest="map_upload_name",
+        action="store",
+        type=str,
+        default=None,
+        required=False,
+        help="The name of the map to use."
+    )
+    parser.add_argument(
+        "-u",
+        "--uptake_constraints_file",
+        dest="uptake_constraints_file",
+        action="store",
+        type=str,
+        default=None,
+        required=False,
+        help="File containing new uptake constraits."
+    )
+    parser.add_argument(
+        "-output",
+        "--output",
+        dest="out_file",
+        action="store",
+        type=str,
+        default=None,
+        required=True,
+        help="The output file."
+    )
+
+    args = parser.parse_args()
+
+    if args.expect_map not in ["True", "False"]:
+        raise Exception("The expect_map argument must be either True or False.")
+    if args.expect_map == "True" and args.map_load_name is None and \
+            args.map_upload_name is None:
+        raise Exception(
+            "You must specify a map name if a map is expected to be uploaded."
+        )
+
+    cb_model = None
+    model_name = None
+    if args.model_to_download is not None and args.model_to_download != "None":
+        if args.cb_model_location is not None \
+                and args.cb_model_location != "None":
+            raise Exception(
+                "You cannot specify both a model to "
+                "download and a model to use."
+            )
+        model_name = args.model_to_download
+    elif args.cb_model_location is not None\
+            and args.cb_model_location != "None":
+        try:
+            cb_model = cobra.io.read_sbml_model(args.cb_model_location)
+        except Exception as e:
+            raise Exception(
+                "The model could not be read. "
+                "Ensure it is in correct SBML format."
+            ) from e
+
+    map_name = None
+    map_location = None
+    if args.map_upload_name is not None and args.map_upload_name != "None":
+        if args.map_load_name is not None and args.map_load_name != "None":
+            raise Exception(
+                "You cannot specify both a map to upload and a map to load."
+            )
+        map_location = args.map_upload_name
+    elif args.map_load_name is not None and args.map_load_name != "None":
+        map_name = args.map_load_name
+
+    if args.uptake_constraints_file is not None and \
+            args.uptake_constraints_file != "None":
+        if cb_model is None:
+            raise Exception(
+                "You cannot specify uptake constraints "
+                "without uploading a model."
+            )
+        else:
+            constraints_df = pd.read_csv(
+                args.uptake_constraints_file,
+                sep=";",
+                header=0,
+                index_col=False
+            )
+            for index, row in constraints_df.iterrows():
+                rxn_id = row["reaction_id"]
+                cb_model.reactions.get_by_id(rxn_id).lower_bound = \
+                    row["lower_bound"]
+                cb_model.reactions.get_by_id(rxn_id).upper_bound = \
+                    row["upper_bound"]
+
+    flux_dict = None
+    if args.flux_distribution_location is not None and \
+            args.flux_distribution_location != "None":
+        if cb_model is None:
+            raise Exception(
+                "You cannot specify a flux distribution "
+                "without uploading a model."
+            )
+        if args.uptake_constraints_file is not None and \
+                args.uptake_constraints_file != "None":
+            raise Exception(
+                "You cannot specify both uptake constraints and a flux "
+                "distribution."
+            )
+        try:
+            flux_df = pd.read_csv(
+                args.flux_distribution_location,
+                sep=";",
+                header=0,
+                index_col=False
+            )
+            flux_dict = {
+                key: value for key, value in zip(
+                    flux_df['reaction_name'],
+                    flux_df['flux']
+                )
+            }
+        except Exception as e:
+            raise Exception(
+                "The flux distribution file could not be read. "
+                "Ensure the file has semicolon-separated "
+                "columns and a header row."
+            ) from e
+
+    if cb_model is not None and flux_dict is None:
+        solution = cobra.flux_analysis.pfba(cb_model)
+
+        # make a dataframe with the reaction names, reaction ids, and flux
+        flux_distribution = pd.DataFrame(
+            columns=["reaction_name", "reaction_id", "flux"]
+        )
+        flux_distribution["reaction_name"] = [
+            reaction.name for reaction in cb_model.reactions
+        ]
+        flux_distribution["reaction_id"] = [
+            reaction.id for reaction in cb_model.reactions
+        ]
+        flux_distribution["flux"] = [
+            solution.fluxes[reaction.id] for reaction in cb_model.reactions
+        ]
+        flux_dict = {
+            key: value for key, value in zip(
+                flux_distribution['reaction_name'],
+                flux_distribution['flux']
+            )
+        }
+
+    builder = Builder()
+    if map_name is not None:
+        builder.map_name = map_name
+        print("Downloading map...")
+    if map_location is not None:
+        builder.map_json = map_location
+        print("Uploading map...")
+    if model_name is not None:
+        builder.model_name = model_name
+        print("Downloading model...")
+    if cb_model is not None:
+        builder.model = cb_model
+        print("Uploading model...")
+
+    if flux_dict is not None:
+        builder.reaction_data = flux_dict
+
+    builder.save_html(args.out_file)
+
+
+if __name__ == "__main__":
+    __main__()