--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/gsalkronapy.nf	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,58 @@
+// Help text for `gen_salmon_tph_and_krona_tsv.py` (gsalkronapy) within CPIPES.
+
+def gsalkronapyHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'gsalkronapy_run': [
+            clihelp: 'Run the `gen_salmon_tph_and_krona_tsv.py` script. Default: ' +
+                (params.gsalkronapy_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'gsalkronapy_sf': [
+            clihelp: 'Set the scaling factor by which TPM values ' +
+                'are scaled down.' +
+                " Default: ${params.gsalkronapy_sf}",
+            cliflag: '-sf',
+            clivalue: (params.gsalkronapy_sf ?: '')
+        ],
+        'gsalkronapy_smres_suffix': [
+            clihelp: 'Find the `sourmash gather` result files ' +
+                'ending in this suffix.' +
+                " Default: ${params.gsalkronapy_smres_suffix}",
+            cliflag: '-smres-suffix',
+            clivalue: (params.gsalkronapy_smres_suffix ?: '')
+        ],
+        'gsalkronapy_failed_suffix': [
+            clihelp: 'Find the sample names which failed classification stored ' +
+                'inside the files ending in this suffix.' +
+                " Default: ${params.gsalkronapy_failed_suffix}",
+            cliflag: '-failed-suffix',
+            clivalue: (params.gsalkronapy_failed_suffix ?: '')
+        ],
+        'gsalkronapy_num_lin_cols': [
+            clihelp: 'Number of columns expected in the lineages CSV file. ' +
+                " Default: ${params.gsalkronapy_num_lin_cols}",
+            cliflag: '-num-lin-cols',
+            clivalue: (params.gsalkronapy_num_lin_cols ?: '')
+        ],
+        'gsalkronapy_lin_regex': [
+            clihelp: 'Number of columns expected in the lineages CSV file. ' +
+                " Default: ${params.gsalkronapy_num_lin_cols}",
+            cliflag: '-num-lin-cols',
+            clivalue: (params.gsalkronapy_num_lin_cols ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
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