adding gem_tools

tools/gem_tools/.shed.yml

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+name: gem_tools
+owner: iuc
+categories:
+  - Metabolomics
+  - Systems Biology
+  - Flux Balance Analysis
+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.py

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+import argparse
+import subprocess
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        prog="MemoteReport",
+        description="This program takes a memote snapshot report of a GEM",
+        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=True,
+        help="The model to use."
+    )
+    parser.add_argument(
+        "-o",
+        "--output",
+        dest="out_file",
+        action="store",
+        type=str,
+        default=None,
+        required=True,
+        help="The output file."
+    )
+
+    output_location = parser.parse_args().out_file
+    cb_model_location = parser.parse_args().cb_model_location
+
+    command = (
+        f"memote report snapshot --filename '{output_location}' "
+        f"'{cb_model_location}'"
+    )
+    try:
+        # Execute the command
+        result = subprocess.run(
+            command,
+            shell=True,
+            check=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True
+        )
+
+        # Output the result
+        print("Command executed successfully.")
+        print("Output:\n", result.stdout)
+    except subprocess.CalledProcessError as e:
+        # Handle errors in the subprocess
+        if "Error:" in e.stderr or "error:" in e.stderr:
+            raise Exception(e.stderr)
+        else:
+            print(e.stderr)
+
+
+if __name__ == "__main__":
+    __main__()

tools/gem_tools/gem_check_memote.xml

@@ -0,0 +1,79 @@
+<tool id="gem_check_memote" name="GEM check memote" version="0.17.0" profile="23.0">
+  <description>Uses the Memote test suite to generate a quality report on a genome-scale metabolic model. See more at https://memote.readthedocs.io/en/latest/index.html</description>
+  <macros>
+    <import>gem_macros.xml</import>
+  </macros>
+  <requirements>
+    <requirement type="package" version="0.17.0">memote</requirement>
+    <requirement type="package" version="2.0.1">markupsafe</requirement>
+  </requirements>
+  <expand macro="version_command_memote"/>
+  <command>
+    python '$__tool_directory__/gem_check_memote.py' '--cb_model_location' '${cb_model_location}' '--output' '${output}'
+  </command>
+  <inputs>
+    <expand macro="input_model"/>
+  </inputs>
+  <outputs>
+    <data name="output" format="html" label="Memote report"/>
+  </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>
+    <citation type="bibtex">
+      @article{lieven2020memote,
+        title={MEMOTE for standardized genome-scale metabolic model testing},
+        author={Lieven, Christian and Beber, Moritz E and Olivier, Brett G and Bergmann, Frank T and Ataman, Meric and Babaei, Parizad and Bartell, Jennifer A and Blank, Lars M and Chauhan, Siddharth and Correia, Kevin and others},
+        journal={Nature biotechnology},
+        volume={38},
+        number={3},
+        pages={272--276},
+        year={2020},
+        publisher={Nature Publishing Group US New York}
+      }
+    </citation>
+  </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(
+        "-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()
+
+    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__()