--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/sourmashsketch.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,73 @@
+// Help text for sourmash sketch dna within CPIPES.
+
+def sourmashsketchHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'sourmashsketch_run': [
+            clihelp: 'Run `sourmash sketch dna` tool. Default: ' +
+                (params.sourmashsketch_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'sourmashsketch_mode': [
+            clihelp: "Select which type of signatures to be created: dna, protein, fromfile or translate. "
+                + "Default: ${params.sourmashsketch_mode}",
+            cliflag: "${params.sourmashsketch_mode}",
+            clivalue: ' '
+        ],
+        'sourmashsketch_p': [
+            clihelp: 'Signature parameters to use. ' +
+                "Default: ${params.sourmashsketch_p}",
+            cliflag: '-p',
+            clivalue: (params.sourmashsketch_p ?: '')
+        ],
+        'sourmashsketch_file': [
+            clihelp: '<path>  A text file containing a list of sequence files to load. ' +
+                "Default: ${params.sourmashsketch_file}",
+            cliflag: '--from-file',
+            clivalue: (params.sourmashsketch_file ?: '')
+        ],
+        'sourmashsketch_f': [
+            clihelp: 'Recompute signatures even if the file exists. ' +
+                "Default: ${params.sourmashsketch_f}",
+            cliflag: '-f',
+            clivalue: (params.sourmashsketch_f ? ' ' : '')
+        ],
+        'sourmashsketch_merge': [
+            clihelp: 'Merge all input files into one signature file with the specified name. ' +
+                "Default: ${params.sourmashsketch_merge}",
+            cliflag: '--merge',
+            clivalue: (params.sourmashsketch_merge ? ' ' : '')
+        ],
+        'sourmashsketch_singleton': [
+            clihelp: 'Compute a signature for each sequence record individually. ' +
+                "Default: ${params.sourmashsketch_singleton}",
+            cliflag: '--singleton',
+            clivalue: (params.sourmashsketch_singleton ? ' ' : '')
+        ],
+        'sourmashsketch_name': [
+            clihelp: 'Name the signature generated from each file after the first record in the file. ' +
+                "Default: ${params.sourmashsketch_name}",
+            cliflag: '--name-from-first',
+            clivalue: (params.sourmashsketch_name ? ' ' : '')
+        ],
+        'sourmashsketch_randomize': [
+            clihelp: 'Shuffle the list of input files randomly. ' +
+                "Default: ${params.sourmashsketch_randomize}",
+            cliflag: '--randomize',
+            clivalue: (params.sourmashsketch_randomize ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file