--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.7.0/lib/help/wsnp.nf	Mon Jul 15 10:42:02 2024 -0400
@@ -0,0 +1,81 @@
+// Help text for waterfall_per_snp_cluster.pl (wsnp) within CPIPES.
+
+def wsnpHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'wsnp_serocol': [
+            clihelp: 'Column number (non 0-based index) of the PDG metadata file ' +
+                'by which the serotypes are collected.' +
+                " Default: ${params.wsnp_serocol}",
+            cliflag: '--serocol',
+            clivalue: (params.wsnp_serocol ?: '')
+        ],
+        'wsnp_seronamecol': [
+            clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
+                'name is "serovar". ' +
+                " Default: ${params.wsnp_seronamecol}",
+            cliflag: '--seronamecol',
+            clivalue: (params.wsnp_seronamecol ?: '')
+        ],
+        'wsnp_acc_col': [
+            clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
+                'name is "acc". ' +
+                " Default: ${params.wsnp_seronamecol}",
+            cliflag: '--acc_col',
+            clivalue: (params.wsnp_acc_col ?: '')
+        ],
+        'wsnp_target_acc_col': [
+            clihelp: 'Column number (non 0-based index) of the PDG metadata file whose column ' +
+                'name is "target_acc". ' +
+                " Default: ${params.wsnp_seronamecol}",
+            cliflag: '--target_acc_col',
+            clivalue: (params.wsnp_target_acc_col ?: '')
+        ],
+        'wsnp_complete_sero': [
+            clihelp: 'Skip indexing serotypes when the serotype name in the column ' +
+                'number 49 (non 0-based) of PDG metadata file consists a "-". For example, if ' +
+                'an accession has a serotype= string as such in column ' +
+                'number 49 (non 0-based): ' +
+                '"serotype=- 13:z4,z23:-" ' +
+                'then, the indexing of that accession is skipped.' +
+                " Default: ${params.wsnp_complete_sero}",
+            cliflag: '--complete_serotype_name',
+            clivalue: (params.wsnp_complete_sero ? ' ' : '')
+        ],
+        'wsnp_not_null_serovar': [
+            clihelp: 'Only index the computed_serotype column ' +
+                'i.e. column number 49 (non 0-based), if the serovar column' +
+                ' is not NULL. ' +
+                " Default: ${params.wsnp_not_null_serovar}",
+            cliflag: '--not_null_serotype_name',
+            clivalue: (params.wsnp_not_null_serovar ?: '')
+        ],
+        'wsnp_i': [
+            clihelp: 'Force include this serovar. Ignores ' +
+                '--wsnp_complete_sero for only this serovar. ' +
+                'Mention multiple serovars separated by a ! (Exclamation mark). ' +
+                'Ex: --wsnp_complete_sero I 4,[5],12:i:-!Agona' +
+                " Default: ${params.wsnp_i}",
+            cliflag: '-i',
+            clivalue: (params.wsnp_i ? params.wsnp_i.split(/\!/).join(' -i ').trim().replace(/^\-i\s+/, '') : '')
+        ],
+        'wsnp_num': [
+            clihelp: 'Number of genome accessions to collect per SNP cluster.' +
+                " Default: ${params.wsnp_num}",
+            cliflag: '-num',
+            clivalue: (params.wsnp_num ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
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