--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/lib/help/dpubmlstpy.nf	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,73 @@
+// Help text for dl_pubmlst_profiles_and_schemes.py (dpubmlstpy) within CPIPES.
+
+def dpubmlstpyHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'dpubmlstpy_run': [
+            clihelp: 'Run the dl_pubmlst_profiles_and_schemes.py ' +
+                'script. Default: ' +
+                (params.dpubmlstpy_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'dpubmlstpy_org': [
+            clihelp: 'The organism name to download the MLST alleles ' +
+                'FASTA and profile CSV for. ' +
+                " Default: ${params.dpubmlstpy_org}",
+            cliflag: '-org',
+            clivalue: (params.dpubmlstpy_org ?: '')
+        ],
+        'dpubmlstpy_mlsts': [
+            clihelp: 'The MLST scheme ID to download. ' +
+                " Default: ${params.dpubmlstpy_mlsts}",
+            cliflag: '-mlsts',
+            clivalue: (params.dpubmlstpy_mlsts ?: '')
+        ],
+        'dpubmlstpy_profile': [
+            clihelp: 'The MLST profile name in the scheme. ' +
+                " Default: ${params.dpubmlstpy_profile}",
+            cliflag: '-profile',
+            clivalue: (params.dpubmlstpy_profile ?: '')
+        ],
+        'dpubmlstpy_loci': [
+            clihelp: 'The key name in the JSON response which lists the ' +
+                'allele URLs to download. ' +
+                " Default: ${params.dpubmlstpy_loci}",
+            cliflag: '-loci',
+            clivalue: (params.dpubmlstpy_loci ?: '')
+        ],
+        'dpubmlstpy_suffix': [
+            clihelp: 'What should be the suffix of the downloaded allele ' +
+                'FASTA. ' +
+                " Default: ${params.dpubmlstpy_suffix}",
+            cliflag: '-suffix',
+            clivalue: (params.dpubmlstpy_suffix ?: '')
+        ],
+        'dpubmlstpy_akey': [
+            clihelp: 'What is the key in the JSON response that contains ' +
+                'the URL for allele FASTA. ' +
+                " Default: ${params.dpubmlstpy_akey}",
+            cliflag: '-akey',
+            clivalue: (params.dpubmlstpy_akey ?: '')
+        ],
+        'dpubmlstpy_id': [
+            clihelp: 'What is the key in the JSON response that contains ' +
+                'the name of the allele FASTA. ' +
+                " Default: ${params.dpubmlstpy_id}",
+            cliflag: '-id',
+            clivalue: (params.dpubmlstpy_id ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file