--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.7.0/lib/help/sourmashsigkmers.nf	Mon Jul 15 10:42:02 2024 -0400
@@ -0,0 +1,97 @@
+// Help text for sourmash sigkmers within CPIPES.
+
+def sourmashsigkmersHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'sourmashsigkmers_run': [
+            clihelp: 'Run `sourmash sigkmers` tool. Default: ' +
+                (params.sourmashsigkmers_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'sourmashsigkmers_k': [
+            clihelp: 'The k-mer size to select. ' +
+                "Default: ${params.sourmashsigkmers_k}",
+            cliflag: '-k',
+            clivalue: (params.sourmashsigkmers_k ?: '')
+        ],
+        'sourmashsigkmers_protein': [
+            clihelp: 'Choose a protein signature. ' +
+                "Default: ${params.sourmashsigkmers_protein}",
+            cliflag: '--protein',
+            clivalue: (params.sourmashsigkmers_protein ? ' ' : '')
+        ],
+        'sourmashsigkmers_noprotein': [
+            clihelp: 'Do not choose a protein signature. ' +
+                "Default: ${params.sourmashsigkmers_noprotein}",
+            cliflag: '--no-protein',
+            clivalue: (params.sourmashsigkmers_noprotein ? ' ' : '')
+        ],
+        'sourmashsigkmers_dayhoff': [
+            clihelp: 'Choose Dayhoff-encoded amino acid signatures. ' +
+                "Default: ${params.sourmashsigkmers_dayhoff}",
+            cliflag: '--dayhoff',
+            clivalue: (params.sourmashsigkmers_dayhoff ? ' ' : '')
+        ],
+        'sourmashsigkmers_nodayhoff': [
+            clihelp: 'Do not choose Dayhoff-encoded amino acid signatures. ' +
+                "Default: ${params.sourmashsigkmers_nodayhoff}",
+            cliflag: '--no-dayhoff',
+            clivalue: (params.sourmashsigkmers_nodayhoff ? ' ' : '')
+        ],
+        'sourmashsigkmers_hp': [
+            clihelp: 'Choose hydrophobic-polar-encoded amino acid signatures. ' +
+                "Default: ${params.sourmashsigkmers_hp}",
+            cliflag: '--hp',
+            clivalue: (params.sourmashsigkmers_hp ? ' ' : '')
+        ],
+        'sourmashsigkmers_nohp': [
+            clihelp: 'Do not choose hydrophobic-polar-encoded amino acid signatures. ' +
+                "Default: ${params.sourmashsigkmers_nohp}",
+            cliflag: '--no-hp',
+            clivalue: (params.sourmashsigkmers_nohp ? ' ' : '')
+        ],
+        'sourmashsigkmers_dna': [
+            clihelp: 'Choose DNA signature. ' +
+                "Default: ${params.sourmashsigkmers_dna}",
+            cliflag: '--dna',
+            clivalue: (params.sourmashsigkmers_dna ? ' ' : '')
+        ],
+        'sourmashsigkmers_nodna': [
+            clihelp: 'Do not choose DNA signature. ' +
+                "Default: ${params.sourmashsigkmers_nodna}",
+            cliflag: '--no-dna',
+            clivalue: (params.sourmashsigkmers_nodna ? ' ' : '')
+        ],
+        'sourmashsigkmers_save_kmers': [
+            clihelp: 'Save k-mers and hash values to a CSV file. ' +
+                "Default: ${params.sourmashsigkmers_save_kmers}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'sourmashsigkmers_save_seqs': [
+            clihelp: 'Save sequences with matching hash values to a FASTA file. ' +
+                "Default: ${params.sourmashsigkmers_save_seqs}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'sourmashsigkmers_translate': [
+            clihelp: 'Translate DNA k-mers into amino acids (for protein, dayhoff, and hp sketches). ' +
+                "Default: ${params.sourmashsigkmers_translate}",
+            cliflag: '--translate',
+            clivalue: (params.sourmashsigkmers_translate ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file