Skip to content

Commit e280536

Browse files
fcyufcyu
committed
Rename a checkbox in Skyline tab to make it more clear.
1 parent f497200 commit e280536

File tree

148 files changed

+167
-168
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

148 files changed

+167
-168
lines changed

‎MSFragger-GUI/src/com/dmtavt/fragpipe/FragpipeRun.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2174,7 +2174,7 @@ private static boolean configureTaskGraph(JComponent parent, Path wd, Path jarPa
21742174
final CmdSkyline cmdSkyline = new CmdSkyline(skylinePanel.isRun(), wd);
21752175
addConfig.accept(cmdSkyline, () -> {
21762176
if (cmdSkyline.isRun()) {
2177-
return cmdSkyline.configure(parent, skylinePanel.getSkylinePath(), skylinePanel.getSkylineVersion(), jarPath, ramGb, diannPanel.isRun(), skylinePanel.getModsMode(), skylinePanel.isOverridePeakBounds());
2177+
return cmdSkyline.configure(parent, skylinePanel.getSkylinePath(), skylinePanel.getSkylineVersion(), jarPath, ramGb, diannPanel.isRun(), skylinePanel.getModsMode(), skylinePanel.isUseSsl());
21782178
}
21792179
return true;
21802180
});

‎MSFragger-GUI/src/com/dmtavt/fragpipe/cmd/CmdSkyline.java

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -22,11 +22,7 @@
2222
import com.dmtavt.fragpipe.Fragpipe;
2323
import com.dmtavt.fragpipe.FragpipeLocations;
2424
import com.dmtavt.fragpipe.Version;
25-
import com.dmtavt.fragpipe.tools.diann.DiannPanel;
26-
import com.dmtavt.fragpipe.tools.ionquant.QuantPanelLabelfree;
2725
import com.dmtavt.fragpipe.tools.skyline.Skyline;
28-
import com.dmtavt.fragpipe.tools.skyline.SkylineMode;
29-
import com.dmtavt.fragpipe.tools.speclibgen.SpeclibPanel;
3026
import com.github.chhh.utils.OsUtils;
3127
import java.awt.Component;
3228
import java.io.IOException;
@@ -56,7 +52,7 @@ public String getCmdName() {
5652
return NAME;
5753
}
5854

59-
public boolean configure(Component comp, String skylinePath, String skylineVersion, Path jarFragpipe, int ramGb, boolean isRunDIANN, int modsMode, boolean overridePeakBounds) {
55+
public boolean configure(Component comp, String skylinePath, String skylineVersion, Path jarFragpipe, int ramGb, boolean isRunDIANN, int modsMode, boolean useSsl) {
6056
initPreConfig();
6157

6258
if (skylinePath == null) {
@@ -112,7 +108,7 @@ public boolean configure(Component comp, String skylinePath, String skylineVersi
112108
cmd.add(skylineVersion);
113109
cmd.add(String.valueOf(isRunDIANN));
114110
cmd.add(String.valueOf(modsMode));
115-
cmd.add(String.valueOf(overridePeakBounds));
111+
cmd.add(String.valueOf(useSsl));
116112

117113
ProcessBuilder pb = new ProcessBuilder(cmd);
118114
pb.directory(wd.toFile());

‎MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -99,7 +99,7 @@ public static void main(String[] args) {
9999
}
100100
}
101101

102-
private static void runSkyline(String skylinePath, Path wd, String skylineVersion, boolean isRunDIANN, int modsMode, boolean overridePeakBounds) throws Exception {
102+
private static void runSkyline(String skylinePath, Path wd, String skylineVersion, boolean isRunDIANN, int modsMode, boolean useSsl) throws Exception {
103103
if (skylinePath == null || skylinePath.isEmpty()) {
104104
throw new RuntimeException("Cannot find the Skyline executable file.");
105105
} else {
@@ -124,7 +124,7 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio
124124
}
125125
}
126126
reader.close();
127-
boolean useSpeclib = isRunDIANN && !overridePeakBounds;
127+
boolean useSpeclib = isRunDIANN && !useSsl;
128128

129129
reader = Files.newBufferedReader(wd.resolve("fragpipe-files.fp-manifest"));
130130
while ((line = reader.readLine()) != null) {
@@ -169,9 +169,9 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio
169169
sslWriter = new WriteSSL();
170170
if (dataType.contentEquals("DIA")) {
171171
// psm.tsv refers to DDA files, need to provide as well
172-
sslWriter.writeSSL(psmTsvFiles, sslPath, isPercolator, ddaAndDIAfiles, !overridePeakBounds);
172+
sslWriter.writeSSL(psmTsvFiles, sslPath, isPercolator, ddaAndDIAfiles, !useSsl);
173173
} else {
174-
sslWriter.writeSSL(psmTsvFiles, sslPath, isPercolator, lcmsFiles, !overridePeakBounds);
174+
sslWriter.writeSSL(psmTsvFiles, sslPath, isPercolator, lcmsFiles, !useSsl);
175175
}
176176
}
177177

‎MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/SkylinePanel.java

Lines changed: 16 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -19,14 +19,17 @@
1919

2020
import static com.github.chhh.utils.OsUtils.isWindows;
2121

22-
import com.dmtavt.fragpipe.Fragpipe;
2322
import com.dmtavt.fragpipe.messages.MessageUiRevalidate;
24-
import com.dmtavt.fragpipe.tools.diann.DiannPanel;
25-
import com.dmtavt.fragpipe.tools.speclibgen.SpeclibPanel;
2623
import com.github.chhh.utils.SwingUtils;
27-
import com.github.chhh.utils.swing.*;
24+
import com.github.chhh.utils.swing.FileChooserUtils;
2825
import com.github.chhh.utils.swing.FileChooserUtils.FcMode;
29-
26+
import com.github.chhh.utils.swing.FormEntry;
27+
import com.github.chhh.utils.swing.JPanelBase;
28+
import com.github.chhh.utils.swing.UiCheck;
29+
import com.github.chhh.utils.swing.UiCombo;
30+
import com.github.chhh.utils.swing.UiRadio;
31+
import com.github.chhh.utils.swing.UiText;
32+
import com.github.chhh.utils.swing.UiUtils;
3033
import java.awt.BorderLayout;
3134
import java.awt.Component;
3235
import java.awt.ItemSelectable;
@@ -64,7 +67,7 @@ public class SkylinePanel extends JPanelBase {
6467
private UiRadio uiRadioSkylineDaily;
6568
private UiRadio uiRadioSkylineCustom;
6669
private UiText uiTextSkylineCustom;
67-
private UiCheck uiCheckOverridePeakBounds;
70+
private UiCheck uiCheckUseSsl;
6871
private UiCombo uiComboModsMode;
6972

7073
@Override
@@ -162,9 +165,9 @@ private JPanel createPanelBasic() {
162165
+ "Check the box to override those bounds and have Skyline calculate its own peak boundaries<br>"
163166
+ "(note: this does NOT affect the output tables from FragPipe).<br>"
164167
+ "If IonQuant/DIANN are not run, Skyline bounds will be used regardless of this setting.";
165-
uiCheckOverridePeakBounds = UiUtils.createUiCheck("Let Skyline override peak bounds", false);
166-
uiCheckOverridePeakBounds.setName("override-peak-bounds");
167-
uiCheckOverridePeakBounds.setToolTipText(SwingUtils.makeHtml(peakBoundsTooltip));
168+
uiCheckUseSsl = UiUtils.createUiCheck("Let Skyline build the library and determine peak boundaries", false);
169+
uiCheckUseSsl.setName("use-ssl");
170+
uiCheckUseSsl.setToolTipText(SwingUtils.makeHtml(peakBoundsTooltip));
168171

169172
uiComboModsMode = UiUtils.createUiCombo(Arrays.asList("Default", "O-glyco", "N-glyco"));
170173
uiComboModsMode.setSelectedIndex(0);
@@ -178,9 +181,9 @@ private JPanel createPanelBasic() {
178181
mu.add(panelBasic, feSkylineCustom.comp).growX().pushX();
179182
mu.add(panelBasic, jButtonSkylineCustom).wrap();
180183

181-
mu.add(panelBasic, uiCheckOverridePeakBounds).wrap();
184+
mu.add(panelBasic, uiCheckUseSsl).wrap();
182185

183-
mu.add(panelBasic, feComboModsMode.label(), mu.ccL());
186+
mu.add(panelBasic, feComboModsMode.label(), mu.ccL()).split(2);
184187
mu.add(panelBasic, feComboModsMode.comp).wrap();
185188

186189
updateEnabledStatus(feSkylineCustom.comp, uiRadioSkylineCustom.isSelected());
@@ -271,8 +274,8 @@ public String getSkylineVersion() {
271274
}
272275
}
273276

274-
public boolean isOverridePeakBounds() {
275-
return uiCheckOverridePeakBounds.isSelected();
277+
public boolean isUseSsl() {
278+
return uiCheckUseSsl.isSelected();
276279
}
277280

278281
public int getModsMode() {

‎MSFragger-GUI/src/resources/workflows/DIA_DIA-Umpire_SpecLib_Quant.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/DIA_SpecLib_Quant.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/DIA_SpecLib_Quant_Phospho.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/DIA_SpecLib_Quant_Phospho_diaPASEF.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/DIA_SpecLib_Quant_diaPASEF.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Default.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Diagnostic-ion-mining.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/FPOP.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/LFQ-MBR.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/LFQ-phospho.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/LFQ-ubiquitin.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Labile_ADP-ribosylation.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Labile_phospho.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Mass-Offset-CommonPTMs.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Nonspecific-HLA-C57.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Nonspecific-HLA-DIA-Astral.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Nonspecific-HLA-DIA.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Nonspecific-HLA-TMT10.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Nonspecific-HLA-diaPASEF.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Nonspecific-HLA-glyco.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=true
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Nonspecific-HLA-phospho.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=3
282282
saintexpress.run-saint-express=true
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Nonspecific-HLA.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Nonspecific-peptidome.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=3
282282
saintexpress.run-saint-express=true
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Open-quickscan.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/Open.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/PAL.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=10
282282
saintexpress.run-saint-express=false
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/SILAC3-phospho.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=3
282282
saintexpress.run-saint-express=true
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/SILAC3.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=3
282282
saintexpress.run-saint-express=true
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

‎MSFragger-GUI/src/resources/workflows/SLC-ABPP.workflow

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ saintexpress.cmd-opts=
281281
saintexpress.max-replicates=3
282282
saintexpress.run-saint-express=true
283283
saintexpress.virtual-controls=100
284-
skyline.override-peak-bounds=false
284+
skyline.use-ssl=false
285285
skyline.run-skyline=false
286286
skyline.skyline=false
287287
skyline.skyline-custom=false

0 commit comments

Comments
 (0)