From a169b585cc54bcb83f4c2691be661171283acf4b Mon Sep 17 00:00:00 2001
From: Katherine Heal <katherine.heal@pnnl.gov>
Date: Fri, 15 Nov 2024 12:18:33 -0800
Subject: [PATCH] Readd metaMS_gcms.wdl, mistakenly removed

---
 wdl/metaMS_gcms.wdl | 46 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 wdl/metaMS_gcms.wdl

diff --git a/wdl/metaMS_gcms.wdl b/wdl/metaMS_gcms.wdl
new file mode 100644
index 0000000..2c812f9
--- /dev/null
+++ b/wdl/metaMS_gcms.wdl
@@ -0,0 +1,46 @@
+version 1.0
+
+workflow gcmsMetabolomics {
+    call runMetaMSGCMS
+
+    output {
+        String out = runMetaMSGCMS.out
+        File output_file = runMetaMSGCMS.output_file
+        File output_metafile = runMetaMSGCMS.output_metafile
+    }
+}
+
+task runMetaMSGCMS {
+    input {
+        Array[File] file_paths
+        File calibration_file_path
+        String output_directory
+        String output_filename
+        String output_type
+        File corems_toml_path
+        File nmdc_metadata_path
+        Int jobs_count
+    }
+
+    command {
+        metaMS run-gcms-wdl-workflow \
+            ${sep=',' file_paths} \
+            ${calibration_file_path} \
+            ${output_directory} \
+            ${output_filename} \
+            ${output_type} \
+            ${corems_toml_path} \
+            ${nmdc_metadata_path} \
+            --jobs ${jobs_count}
+    }
+
+    output {
+        String out = read_string(stdout())
+        File output_file = "${output_directory}/${output_filename}.${output_type}"
+        File output_metafile = "${output_directory}/${output_filename}.json"
+    }
+
+    runtime {
+        docker: "microbiomedata/metams:2.2.2"
+    }
+}
\ No newline at end of file