Put the --import-file back

fcyu · fcyu · commit efd169dd0b1f · 2024-10-11T12:37:52.000-04:00
Skyline needs the path to locate the LC-MS files not in the work dir. Removed by e960094
diff --git a/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java b/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java
@@ -255,11 +255,8 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio
         writer.write("--full-scan-isolation-scheme=\"Results only\" ");
       }
 
-      if (dataType.contentEquals("DIA") && overridePeakBounds) {
-        // lc-ms file import is automatic when reading peptide list, but needs the DIA files imported separated for DIA SSL
-        for (String s : lcmsFiles) {
-          writer.write("--import-file=" + s + " ");
-        }
+      for (String s : lcmsFiles) {
+        writer.write("--import-file=" + s + " ");
       }
 
       // todo: waiting for a fix (or clarification) from Brendan. Skyline does not allow this unless fasta has been imported

Original file line number	Diff line number	Diff line change
`@@ -255,11 +255,8 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio`
`255`	`255`	`writer.write("--full-scan-isolation-scheme=\"Results only\" ");`
`256`	`256`	`}`
`257`	`257`
`258`		`- if (dataType.contentEquals("DIA") && overridePeakBounds) {`
`259`		`- // lc-ms file import is automatic when reading peptide list, but needs the DIA files imported separated for DIA SSL`
`260`		`- for (String s : lcmsFiles) {`
`261`		`- writer.write("--import-file=" + s + " ");`
`262`		`- }`
	`258`	`+ for (String s : lcmsFiles) {`
	`259`	`+ writer.write("--import-file=" + s + " ");`
`263`	`260`	`}`
`264`	`261`
`265`	`262`	`// todo: waiting for a fix (or clarification) from Brendan. Skyline does not allow this unless fasta has been imported`