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removed default parameters #94

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merged 6 commits into from
Sep 25, 2023
Merged

removed default parameters #94

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943da1b
removed default parameters
viikiid Sep 25, 2023
b5ac9c8
Merge branch 'main' into parameters_error_messages
viikiid Sep 25, 2023
98f2bf5
Merge branch 'main' into parameters_error_messages
viikiid Sep 25, 2023
b37f8af
added interface to upload meta data files #98
viikiid Sep 25, 2023
32b7c64
Merge branch 'main' into parameters_error_messages
RobbinBouwmeester Sep 25, 2023
419d655
Merge branch 'main' into parameters_error_messages
RobbinBouwmeester Sep 25, 2023
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2 changes: 1 addition & 1 deletion webinterface/configuration/dda_quant.json
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"version": {"type": "text_input", "label": "Search engine version", "value": {"MaxQuant": 1.0, "AlphaPept": 1.0, "MSFragger": 1.0, "Proline": 1.0, "WOMBAT": 1.0}}, "software_name": {"type": "text_input", "label": "Search engine name", "value": {"MaxQuant": "MaxQuant", "AlphaPept": "AlphaPept", "MSFragger": "MSFragger", "Proline": "Proline", "WOMBAT": "WOMBAT"}}, "fdr_psm": {"type": "number_input", "label": "FDR psm", "value": {"MaxQuant": 0.01, "AlphaPept": 0.01, "MSFragger": 0.01, "Proline": 0.01, "WOMBAT": 0.01}, "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "fdr_peptide": {"type": "number_input", "label": "FDR peptide", "value": {"MaxQuant": 0.01, "AlphaPept": 0.01, "MSFragger": 0.01, "Proline": 0.01, "WOMBAT": 0.01}, "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "fdr_protein": {"type": "number_input", "label": "FDR protein", "value": {"MaxQuant": 0.01, "AlphaPept": 0.01, "MSFragger": 0.01, "Proline": 0.01, "WOMBAT": 0.01}, "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "precursor_mass_tolerance": {"type": "number_input", "label": "Precursor mass tolerance", "value": {"MaxQuant": 10.0, "AlphaPept": 10.0, "MSFragger": 10.0, "Proline": 10.0, "WOMBAT": 10.0}, "min_value": 0.0, "max_value": 5.0, "format": "%.4f"}, "precursor_mass_tolerance_unit": {"type": "selectbox", "label": "Precursor tolerance unit", "value": {"MaxQuant": "PPM", "AlphaPept": "PPM", "MSFragger": "PPM", "Proline": "PPM", "WOMBAT": "PPM"}, "options": ["PPM", "Da"]}, "fragment_mass_tolerance": {"type": "number_input", "label": "Fragment mass tolerance", "value": {"MaxQuant": 10.0, "AlphaPept": 10.0, "MSFragger": 10.0, "Proline": 10.0, "WOMBAT": 10.0}, "min_value": 0.0, "max_value": 5.0, "format": "%.4f"}, "fragment_mass_tolerance_unit": {"type": "selectbox", "label": "Fragment mass tolerance unit", "value": {"MaxQuant": "PPM", "AlphaPept": "PPM", "MSFragger": "PPM", "Proline": "PPM", "WOMBAT": "PPM"}, "options": ["PPM", "Da"]}, "search_enzyme_name": {"type": "selectbox", "label": "Enzyme", "value": {"MaxQuant": "Trypsin", "AlphaPept": "Trypsin", "MSFragger": "Trypsin", "Proline": "Trypsin", "WOMBAT": "Trypsin"}, "options": ["Trypsin", "Chemotrypsin"]}, "allowed_missed_cleavage": {"type": "number_input", "label": "Maximum allowed number of missed cleavage", "value": {"MaxQuant": 2, "AlphaPept": 2, "MSFragger": 2, "Proline": 2, "WOMBAT": 2}, "format": "%d"}, "fixed_mods": {"type": "text_input", "label": "Specify the fixed mods that were set", "value": {"MaxQuant": "CAM", "AlphaPept": "CAM", "MSFragger": "CAM", "Proline": "CAM", "WOMBAT": "CAM"}}, "variable_mods": {"type": "text_input", "label": "Specify the variable mods that were set (separated by a comma)", "value": {"MaxQuant": "MOxid, 'N-term Acetyl'", "AlphaPept": "MOxid, 'N-term Acetyl'", "MSFragger": "MOxid, 'N-term Acetyl'", "Proline": "MOxid, 'N-term Acetyl'", "WOMBAT": "MOxid, 'N-term Acetyl'"}}, "precursor_charge": {"type": "text_input", "label": "Possible charge states (separated by a comma)", "value": {"MaxQuant": "2,3,4,5,6", "AlphaPept": "2,3,4,5,6", "MSFragger": "2,3,4,5,6", "Proline": "2,3,4,5,6", "WOMBAT": "2,3,4,5,6"}}, "max_num_mods_on_peptide": {"type": "number_input", "label": "Maximum number of modifications on peptides", "value": {"MaxQuant": 2, "AlphaPept": 2, "MSFragger": 2, "Proline": 2, "WOMBAT": 2}, "format": "%d"}, "min_peptide_length": {"type": "number_input", "label": "Minimum peptide length", "value": {"MaxQuant": 6, "AlphaPept": 6, "MSFragger": 6, "Proline": 6, "WOMBAT": 6}, "format": "%d"}, "max_peptide_length": {"type": "number_input", "label": "max_peptide_length", "value": {"MaxQuant": 25, "AlphaPept": 25, "MSFragger": 25, "Proline": 25, "WOMBAT": 25}, "format": "%d"}, "mbr": {"type": "checkbox", "label": "Quantified with MBR", "value": {"MaxQuant": true, "AlphaPept": true, "MSFragger": true, "Proline": true, "WOMBAT": true}}, "workflow_description": {"type": "text_area", "label": "Fill in details not specified above, such as:", "value": {"MaxQuant": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...", "AlphaPept": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...", "MSFragger": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...", "Proline": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...", "WOMBAT": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ..."}, "height": 275}}
{"version": {"type": "text_input", "label": "Search engine version", "placeholder" : "1.0"}, "software_name": {"type": "text_input", "label": "Search engine name", "value": {"MaxQuant": "MaxQuant", "AlphaPept": "AlphaPept", "MSFragger": "MSFragger", "Proline": "Proline", "WOMBAT": "WOMBAT"}}, "fdr_psm": {"type": "number_input", "label": "FDR psm", "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "fdr_peptide": {"type": "number_input", "label": "FDR peptide", "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "fdr_protein": {"type": "number_input", "label": "FDR protein", "min_value": 0.0, "max_value": 1.0, "format": "%.4f"}, "precursor_mass_tolerance": {"type": "number_input", "label": "Precursor mass tolerance", "min_value": 0.0, "max_value": 200.0, "format": "%.4f"}, "precursor_mass_tolerance_unit": {"type": "selectbox", "label": "Precursor tolerance unit", "value": {"MaxQuant": "-", "AlphaPept": "-", "MSFragger": "-", "Proline": "-", "WOMBAT": "-"}, "options": ["-", "PPM", "Da"]}, "fragment_mass_tolerance": {"type": "number_input", "label": "Fragment mass tolerance", "min_value": 0.0, "max_value": 100.0, "format": "%.4f"}, "fragment_mass_tolerance_unit": {"type": "selectbox", "label": "Fragment mass tolerance unit", "value": {"MaxQuant": "-", "AlphaPept": "-", "MSFragger": "-", "Proline": "-", "WOMBAT": "-"}, "options": ["-", "PPM", "Da"]}, "search_enzyme_name": {"type": "selectbox", "label": "Enzyme", "value": {"MaxQuant": "-", "AlphaPept": "-", "MSFragger": "-", "Proline": "-", "WOMBAT": "-"}, "options": ["-", "Trypsin", "Chemotrypsin"]}, "allowed_missed_cleavage": {"type": "number_input", "label": "Maximum allowed number of missed cleavage", "min_value": 0, "max_value": 10,"format": "%d"}, "fixed_mods": {"type": "text_input", "label": "Specify the fixed mods that were set", "placeholder": "CAM"}, "variable_mods": {"type": "text_input", "label": "Specify the variable mods that were set (separated by a comma)", "placeholder": "MOxid, N-term Acetyl"}, "precursor_charge": {"type": "text_input", "label": "Possible charge states (separated by a comma)", "placeholder": "2,3,4,5,6"}, "max_num_mods_on_peptide": {"type": "number_input", "label": "Maximum number of modifications on peptides", "min_value": 0, "max_value": 10,"format": "%d"}, "min_peptide_length": {"type": "number_input", "label": "Minimum peptide length", "min_value": 0, "max_value": 100,"format": "%d"}, "max_peptide_length": {"type": "number_input", "label": "Maximum peptide length", "min_value": 0, "max_value": 1000,"format": "%d"}, "mbr": {"type": "checkbox", "label": "Quantified with MBR", "value": {"MaxQuant": false, "AlphaPept": false, "MSFragger": false, "Proline": false, "WOMBAT": false}}, "workflow_description": {"type": "text_area", "label": "Fill in details not specified above", "placeholder": "This workflow was run with isotope errors considering M-1, M+1, and M+2 ...'", "height": 275}}
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Is this file automatically created? Then we might want to format it using indent=2 or indent=4?

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no, from this file all parameters in the UI are generated

16 changes: 13 additions & 3 deletions webinterface/pages/DDA_Quant.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,12 +56,17 @@ def __init__(self):

def generate_input_field(self, input_format: str, content: dict):
if content["type"] == "text_input":
return st.text_input(content["label"], content["value"][input_format])
if "placeholder" in content:
return st.text_input(content["label"], placeholder=content["placeholder"])
elif "value" in content:
return st.text_input(content["label"], content["value"][input_format])
if content["type"] == "number_input":
return st.number_input(
content["label"],
value=content["value"][input_format],
value=None,
format=content["format"],
min_value=content["min_value"],
max_value=content["max_value"]
)
if content["type"] == "selectbox":
return st.selectbox(
Expand Down Expand Up @@ -145,6 +150,7 @@ def _main_page(self):
self.user_input[key] = self.generate_input_field(
self.user_input["input_format"], value
)

submit_button = st.form_submit_button(
"Parse and bench", help=self.texts.Help.additional_parameters
)
Expand All @@ -154,7 +160,11 @@ def _main_page(self):
self._populate_results()

if submit_button:
self._run_proteobench()
if self.user_input["input_csv"]:
self._run_proteobench()
else:
error_message = st.error(":x: Please provide a result file")
print(":x: Proteobench ran into a problem")

def _populate_results(self):
self.generate_results("", None, None, False)
Expand Down