# HG changeset patch
# User iuc
# Date 1761239146 0
# Node ID ec2a1f280d67b76f030712cec6b389d9f88d01a3
# Parent  9fc154508622ea5fb8a3c03bf98001e314506771
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit 1ea9e99e1c7a7cd0f012467466e0740b6bdeb90e

diff -r 9fc154508622 -r ec2a1f280d67 data_manager/salmon_index_builder.xml
--- a/data_manager/salmon_index_builder.xml	Wed Oct 22 14:38:22 2025 +0000
+++ b/data_manager/salmon_index_builder.xml	Thu Oct 23 17:05:46 2025 +0000
@@ -1,8 +1,8 @@
 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
     <description>index builder</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.3.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">1.10.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
         <token name="@PROFILE@">24.0</token>
         <token name="@IDX_VERSION@">q7</token>
     </macros>
@@ -10,6 +10,9 @@
         <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        ## salmon uses one thread to much 
+        SLOTS=\$(( \${GALAXY_SLOTS:-12} > 1 ? \${GALAXY_SLOTS:-12} - 1 : 1 ));
+
         ## https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
         ## https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
         
@@ -27,7 +30,7 @@
             -t gentrome.fa
             -d decoys.txt
             -i '$out_file.extra_files_path'
-            -p "\${GALAXY_SLOTS:-12}"
+            -p "\$SLOTS"
             $gencode
             &&
 
diff -r 9fc154508622 -r ec2a1f280d67 test-data/salmon_indexes_versioned.loc
--- a/test-data/salmon_indexes_versioned.loc	Wed Oct 22 14:38:22 2025 +0000
+++ b/test-data/salmon_indexes_versioned.loc	Thu Oct 23 17:05:46 2025 +0000
@@ -0,0 +1,2 @@
+sequence_id	phiX174	sequence_name	/tmp/tmp1py4xsp5/galaxy-dev/tool-data/phiX174/salmon_index/sequence_id/q7	q7
+phiX174	phiX174	phiX174	/tmp/tmp1py4xsp5/galaxy-dev/tool-data/phiX174/salmon_index/phiX174/q7	q7