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vgp57214_gsk committed Mar 28, 2024
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280 changes: 140 additions & 140 deletions jsons/parameters.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3480,6 +3480,70 @@
},
"value_type": "bool"
},
{
"default_value": false,
"description": "Comma separated list of compensation files",
"key_translations": {
"cytocluster_style_1": "--compensationFiles",
"ursgal_style_1": "compensation_files"
},
"name": "compensation_files",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {
"cytocluster_style_1": [
[
false,
"FALSE"
]
],
"ursgal_style_1": [
[
false,
false
]
]
},
"value_type": "str"
},
{
"default_value": false,
"description": "Is the compensation required? Is the FCS pre-compensated? [TRUE, FALSE]",
"key_translations": {
"cytocluster_style_1": "--compensationRequired",
"ursgal_style_1": "compensation_required"
},
"name": "compensation_required",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {
"cytocluster_style_1": [
[
false,
"FALSE"
],
[
true,
"TRUE"
]
],
"ursgal_style_1": [
[
false,
false
],
[
true,
true
]
]
},
"value_type": "bool"
},
{
"default_value": "com.compomics.util.experiment.identification.protein_inference.executable.PeptideMapping",
"description": "Default value accesses the PeptideMapper tool, other tools are not implemented/covered yet",
Expand Down Expand Up @@ -7614,6 +7678,21 @@
"value_translations": {},
"value_type": "str"
},
{
"default_value": "",
"description": "FCS file to be preprocessed",
"key_translations": {
"cytocluster_style_1": "--fcs",
"ursgal_style_1": "fcs_file"
},
"name": "fcs_file",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"default_value": 0.01,
"description": "Target PSMs with a lower FDR than this threshold will be used as a positive training set for SVM post-processing",
Expand Down Expand Up @@ -8361,6 +8440,21 @@
"value_translations": {},
"value_type": "str_password"
},
{
"default_value": "",
"description": "Gating strategy into a CSV file",
"key_translations": {
"cytocluster_style_1": "--gatingStrategy",
"ursgal_style_1": "gating_strategy"
},
"name": "gating_strategy",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"default_value": true,
"description": "Defines if an output matrix containing information about protein groups, gene groups, unique genes and precursors should be generated.",
Expand Down Expand Up @@ -10043,6 +10137,21 @@
"value_translations": {},
"value_type": "str"
},
{
"default_value": "",
"description": "Directory with QC to plot",
"key_translations": {
"cytocluster_style_1": "--inputDir",
"ursgal_style_1": "input_dir"
},
"name": "input_dir",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"default_value": "q_exactive",
"description": "Type of mass spectrometer (used to determine the scoring model)",
Expand Down Expand Up @@ -13873,6 +13982,21 @@
"value_translations": {},
"value_type": "bool"
},
{
"default_value": "",
"description": "Output directory",
"key_translations": {
"cytocluster_style_1": "--outDir",
"ursgal_style_1": "out_dir"
},
"name": "out_dir",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"default_value": true,
"description": "Output probabilities for each amino acid.",
Expand Down Expand Up @@ -15797,6 +15921,21 @@
"value_translations": {},
"value_type": "float"
},
{
"default_value": "",
"description": "Which QC methods you want to apply on the FCS file",
"key_translations": {
"cytocluster_style_1": "--qcMethod",
"ursgal_style_1": "qc_method"
},
"name": "qc_method",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"default_value": null,
"description": " Molecules to quantify. Can be either a list of strings or a csv file ",
Expand Down Expand Up @@ -21502,144 +21641,5 @@
]
},
"value_type": "bool"
},
{
"description": "FCS file to be preprocessed",
"default_value": "",
"key_translations": {
"cytocluster_style_1": "--fcs",
"ursgal_style_1": "fcs_file"
},
"name": "fcs_file",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"description": "Is the compensation required? Is the FCS pre-compensated? [TRUE, FALSE]",
"default_value": false,
"key_translations": {
"cytocluster_style_1": "--compensationRequired",
"ursgal_style_1": "compensation_required"
},
"name": "compensation_required",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {
"cytocluster_style_1": [
[
false,
"FALSE"
],
[
true,
"TRUE"
]
],
"ursgal_style_1": [
[
true,
true
],
[
false,
false
]
]
},
"value_type": "bool"
},
{
"description": "Comma separated list of compensation files",
"default_value": false,
"key_translations": {
"cytocluster_style_1": "--compensationFiles",
"ursgal_style_1": "compensation_files"
},
"name": "compensation_files",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {
"cytocluster_style_1": [
[
false,
"FALSE"
]
],
"ursgal_style_1": [
[
false,
false
]
]
},
"value_type": "str"
},
{
"description": "Which QC methods you want to apply on the FCS file",
"default_value": "",
"key_translations": {
"cytocluster_style_1": "--qcMethod",
"ursgal_style_1": "qc_method"
},
"name": "qc_method",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"description": "Output directory",
"default_value": "",
"key_translations": {
"cytocluster_style_1": "--outDir",
"ursgal_style_1": "out_dir"
},
"name": "out_dir",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"description": "Directory with QC to plot",
"default_value": "",
"key_translations": {
"cytocluster_style_1": "--inputDir",
"ursgal_style_1": "input_dir"
},
"name": "input_dir",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
},
{
"description": "Gating strategy into a CSV file",
"default_value": "",
"key_translations": {
"cytocluster_style_1": "--gatingStrategy",
"ursgal_style_1": "gating_strategy"
},
"name": "gating_strategy",
"tag": [
"cytocluster"
],
"triggers_rerun": true,
"value_translations": {},
"value_type": "str"
}
]
]
16 changes: 8 additions & 8 deletions jsons/styles.json
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Original file line number Diff line number Diff line change
Expand Up @@ -175,14 +175,6 @@
"versions": [
"1.0.0"
]
},
{
"name": "pymzML",
"reference": " Kösters, M., Leufken, J., Schulze, S., Sugimoto, K., Klein, J., Zahedi, R. P., Hippler, M., Leidel, S. A., & Fufezan, C. (2018).pymzML v2.0: introducing a highly compressed and seekable gzip format. In J. Wren (Ed.), Bioinformatics (Vol. 34, Issue 14, pp. 2513–2514). Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/bty046",
"style": "mzml2idxgz_style_1",
"versions": [
"2.5.2"
]
},
{
"name": "Kallisto 0.48.0",
Expand Down Expand Up @@ -825,6 +817,14 @@
"1.7.4"
]
},
{
"name": "pymzML",
"reference": " K\u00f6sters, M., Leufken, J., Schulze, S., Sugimoto, K., Klein, J., Zahedi, R. P., Hippler, M., Leidel, S. A., & Fufezan, C. (2018).pymzML v2.0: introducing a highly compressed and seekable gzip format. In J. Wren (Ed.), Bioinformatics (Vol. 34, Issue 14, pp. 2513\u20132514). Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/bty046",
"style": "mzml2idxgz_style_1",
"versions": [
"2.5.2"
]
},
{
"name": "pyqms",
"reference": "Leufken J, Niehues A, Sarin LP, Wessel F, Hippler M, Leidel SA, Fufezan C (2017) pyQms enables universal and accurate quantification of mass spectrometry data",
Expand Down

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