--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/wcomp.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,66 @@
+// Help text for waterfall_per_computed_serotype.pl (wcomp) within CPIPES.
+
+def wcompHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'wcomp_serocol': [
+            clihelp: 'Column number (non 0-based index) of the PDG metadata file ' +
+                'by which the serotypes are collected.' +
+                " Default: ${params.wcomp_serocol}",
+            cliflag: '--serocol',
+            clivalue: (params.wcomp_serocol ?: '')
+        ],
+        'wcomp_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.wcomp_complete_sero}",
+            cliflag: '--complete_serotype_name',
+            clivalue: (params.wcomp_complete_sero ? ' ' : '')
+        ],
+        'wcomp_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.wcomp_not_null_serovar}",
+            cliflag: '--not_null_serotype_name',
+            clivalue: (params.wcomp_not_null_serovar ?: '')
+        ],
+        'wcomp_i': [
+            clihelp: 'Force include this serovar. Ignores ' +
+                '--wcomp_complete_sero for only this serovar. ' +
+                'Mention multiple serovars separated by a ! (Exclamation mark). ' +
+                'Ex: --wcomp_complete_sero I 4,[5],12:i:-!Agona' +
+                " Default: ${params.wcomp_i}",
+            cliflag: '-i',
+            clivalue: (params.wcomp_i ? params.wcomp_i.split(/\!/).join(' -i ').trim().replace(/^\-i\s+/, '') : '')
+        ],
+        'wcomp_num': [
+            clihelp: 'Number of genome accessions to be collected per serotype.' +
+                " Default: ${params.wcomp_num}",
+            cliflag: '-num',
+            clivalue: (params.wcomp_num ?: '')
+        ],
+        'wcomp_min_contig_size': [
+            clihelp: 'Minimum contig size to consider a genome for indexing.' +
+                " Default: ${params.wcomp_min_contig_size}",
+            cliflag: '--min_contig_size',
+            clivalue: (params.wcomp_min_contig_size ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
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