--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/lib/help/shovill.nf	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,103 @@
+// Help text for shovill within CPIPES.
+
+def shovillHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'shovill_run': [
+            clihelp: 'Run shovill tool. Default: ' +
+                (params.shovill_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'shovill_depth': [
+            clihelp: 'Sub-sample R1/R2 to this depth. Disable with --shovill_depth 0. ' +
+                "Default: ${params.shovill_depth}",
+            cliflag: '--depth',
+            clivalue: (params.shovill_depth ?: 150)
+        ],
+        'shovill_gsize': [
+            clihelp: 'Estimated genome size eg. 3.2M. <false=AUTODETECT>. ' +
+                "Default: ${params.shovill_gsize}",
+            cliflag: '--gsize',
+            clivalue: (params.shovill_gsize ?: '')
+        ],
+        'shovill_minlen': [
+            clihelp: 'Minimum contig length. <false=AUTO>. ' +
+                "Default: ${params.shovill_minlen}",
+            cliflag: '--minlen',
+            clivalue: (params.shovill_minlen ?: '')
+        ],
+        'shovill_mincov': [
+            clihelp: "Minimum contig coverage. <false=AUTO>. " +
+                "Default: ${params.shovill_mincov}",
+            cliflag: '--mincov',
+            clivalue: (params.shovill_mincov ?: '')
+        ],
+        'shovill_namefmt': [
+            clihelp: "Format of contig FASTA IDs in 'printf' style. " +
+                "Default: ${params.shovill_namefmt}",
+            cliflag: '--namefmt',
+            clivalue: (params.shovill_namefmt ?: '')
+        ],
+        'shovill_keepfiles': [
+            clihelp: 'Keep intermediate files. ' +
+                "Default: ${params.shovill_keepfiles}",
+            cliflag: '--keepfiles',
+            clivalue: (params.shovill_keepfiles ? ' ' : '')
+        ],
+        'shovill_assembler': [
+            clihelp: 'Assembler: skesa, megahit, velvet, or spades. ' +
+                "Default: ${params.shovill_assembler}",
+            cliflag: '--assembler',
+            clivalue: (params.shovill_assembler ?: '')
+        ],
+        'shovill_opts': [
+            clihelp: "Extra assembler options in quotes. Ex: '--sc'. " +
+                "Default: ${params.shovill_opts}",
+            cliflag: '--opts',
+            clivalue: (params.shovill_opts ?: '')
+        ],
+        'shovill_kmers': [
+            clihelp: 'K-mers to use. <false=AUTO>. ' +
+                "Default: ${params.shovill_kmers}",
+            cliflag: '--kmers',
+            clivalue: (params.shovill_kmers ?: '')
+        ],
+        'shovill_trim': [
+            clihelp: 'Enable adator trimming. ' +
+                "Default: ${params.shovill_trim}",
+            cliflag: '--trim',
+            clivalue: (params.shovill_trim ? ' ' : '')
+        ],
+        'shovill_noreadcorr': [
+            clihelp: 'Disable read error correction. ' +
+                "Default: ${params.shovill_noreadcorr}",
+            cliflag: '--noreadcorr',
+            clivalue: (params.shovill_noreadcorr ? ' ' : '')
+        ],
+        'shovill_nostitch': [
+            clihelp: 'Disable read stitching. ' +
+                "Default: ${params.shovill_nostitch}",
+            cliflag: '--nostitch',
+            clivalue: (params.shovill_nostitch ? ' ' : '')
+        ],
+        'shovill_nocorr': [
+            clihelp: 'Disable post-assembly correction. ' +
+                "Default: ${params.shovill_nocorr}",
+            cliflag: '--nocorr',
+            clivalue: (params.shovill_nocorr ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file