--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/sfhpy.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,52 @@
+// Help text for sourmash_filter_hits.py (sfhpy) within CPIPES.
+def sfhpyHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'sfhpy_run': [
+            clihelp: 'Run the sourmash_filter_hits.py ' +
+                'script. Default: ' +
+                (params.sfhpy_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'sfhpy_fcn': [
+            clihelp: 'Column name by which filtering of rows should be applied. ' +
+                "Default: ${params.sfhpy_fcn}",
+            cliflag: '-fcn',
+            clivalue: (params.sfhpy_fcn ?: '')
+        ],
+        'sfhpy_fcv': [
+            clihelp: 'Remove genomes whose match with the query FASTQ is less than ' +
+                'this much. ' +
+                "Default: ${params.sfhpy_fcv}",
+            cliflag: '-fcv',
+            clivalue: (params.sfhpy_fcv ?: '')
+        ],
+        'sfhpy_gt': [
+            clihelp: 'Apply greather than or equal to condition on numeric values of ' +
+                '--sfhpy_fcn column. ' +
+                "Default: ${params.sfhpy_gt}",
+            cliflag: '-gt',
+            clivalue: (params.sfhpy_gt ? ' ' : '')
+        ],
+        'sfhpy_lt': [
+            clihelp: 'Apply less than or equal to condition on numeric values of ' +
+                '--sfhpy_fcn column. ' +
+                "Default: ${params.sfhpy_lt}",
+            cliflag: '-gt',
+            clivalue: (params.sfhpy_lt ? ' ' : '')
+        ],
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file