From e82739e0bba45051d629ad7c460a32911716f68d Mon Sep 17 00:00:00 2001
From: Reid Wagner <wagnerr@umn.edu>
Date: Sat, 29 Jun 2024 12:25:31 +0200
Subject: [PATCH] Use GALAXY_SLOTS for FragPipe --threads argument.

---
 tools/fragpipe/fragpipe.xml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tools/fragpipe/fragpipe.xml b/tools/fragpipe/fragpipe.xml
index 2ac52ff41..223351f26 100644
--- a/tools/fragpipe/fragpipe.xml
+++ b/tools/fragpipe/fragpipe.xml
@@ -37,7 +37,7 @@
                 --msfragger_key f28c4be2-759b0a11-6c1ea652-1240565a
                 --ionquant_key 47cb2953-b4bf7726-2c96f5fe-8f1013aa
                 --headless
-                --threads $threads
+                --threads \${GALAXY_SLOTS:-8}
                 --ram \$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]
                 --workflow fp.workflow --manifest fp.manifest
                 --workdir outputs
@@ -77,8 +77,6 @@
             <option value="combined_outputs">FragPipe Combined Outputs</option>
             <option value="concatenated_outputs">TSV Outputs Concatenated</option>
         </param>
-
-        <param argument="--threads" type="integer" value="8" label="Number of threads"/>
     </inputs>
 
     <outputs>