--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/seqsero2.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,50 @@
+def seqsero2Help(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'seqsero2_run': [
+            clihelp: "Run SeqSero2 tool. Default: ${params.seqsero2_run}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'seqsero2_t': [
+            clihelp: "'1' for interleaved paired-end reads, '2' for " +
+                "separated paired-end reads, '3' for single reads, '4' for " +
+                "genome assembly, '5' for nanopore reads (fasta/fastq). " +
+                "Default: ${params.seqsero2_t}",
+            cliflag: '-t',
+            clivalue: (params.seqsero2_t ?: '')
+        ],
+        'seqsero2_m': [
+            clihelp: "Which workflow to apply, 'a'(raw reads allele " +
+                "micro-assembly), 'k'(raw reads and genome assembly k-mer). " +
+                "Default: ${params.seqsero2_m}",
+            cliflag: '-m',
+            clivalue: (params.seqsero2_m ?: '')
+        ],
+        'seqsero2_c': [
+            clihelp: 'SeqSero2 will only output serotype prediction without the directory ' +
+                'containing log files. ' +
+                "Default: ${params.seqsero2_c}",
+            cliflag: '-c',
+            clivalue: (params.seqsero2_c ? ' ' : '')
+        ],
+        'seqsero2_s': [
+            clihelp: 'SeqSero2 will not output header in SeqSero_result.tsv. ' +
+                "Default: ${params.seqsero2_s}",
+            cliflag: '-l',
+            clivalue: (params.seqsero2_s ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file