--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/kmaindex.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,91 @@
+// Help text for kma index within CPIPES.
+
+def kmaindexHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'kmaindex_run': [
+            clihelp: 'Run kma index tool. Default: ' +
+                (params.kmaindex_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'kmaindex_t_db': [
+            clihelp: 'Add to existing DB. ' +
+                "Default: ${params.kmaindex_t_db}",
+            cliflag: '-t_db',
+            clivalue: (params.kmaindex_t_db ? ' ' : '')
+        ], 
+        'kmaindex_k': [
+            clihelp: 'k-mer size. ' +
+                "Default: ${params.kmaindex_k}",
+            cliflag: '-k',
+            clivalue: (params.kmaindex_k ?: '')
+        ],
+        'kmaindex_m': [
+            clihelp: 'Minimizer size. ' +
+                "Default: ${params.kmaindex_m}",
+            cliflag: '-m',
+            clivalue: (params.kmaindex_m ?: '')
+        ],
+        'kmaindex_hc': [
+            clihelp: 'Homopolymer compression. ' +
+                "Default: ${params.kmaindex_hc}",
+            cliflag: '-hc',
+            clivalue: (params.kmaindex_hc ? ' ' : '')
+        ],
+        'kmaindex_ML': [
+            clihelp: 'Minimum length of templates. Defaults to --kmaindex_k ' +
+                "Default: ${params.kmaindex_ML}",
+            cliflag: '-ML',
+            clivalue: (params.kmaindex_ML ?: '')
+        ],
+        'kmaindex_ME': [
+            clihelp: 'Mega DB. ' +
+                "Default: ${params.kmaindex_ME}",
+            cliflag: '-ME',
+            clivalue: (params.kmaindex_ME ? ' ' : '')
+        ],
+        'kmaindex_Sparse': [
+            clihelp: 'Make Sparse DB. ' +
+                "Default: ${params.kmaindex_Sparse}",
+            cliflag: '-Sparse',
+            clivalue: (params.kmaindex_Sparse ? ' ' : '')
+        ],
+        'kmaindex_ht': [
+            clihelp: 'Homology template. ' +
+                "Default: ${params.kmaindex_ht}",
+            cliflag: '-ht',
+            clivalue: (params.kmaindex_ht ?: '')
+        ],
+        'kmaindex_hq': [
+            clihelp: 'Homology query. ' +
+                "Default: ${params.kmaindex_hq}",
+            cliflag: '-hq',
+            clivalue: (params.kmaindex_hq ?: '')
+        ],
+        'kmaindex_and': [
+            clihelp: 'Both homology thresholds have to reach. ' +
+                "Default: ${params.kmaindex_and}",
+            cliflag: '-and',
+            clivalue: (params.kmaindex_and ? ' ' : '')
+        ],
+        'kmaindex_nbp': [
+            clihelp: 'No bias print. ' +
+                "Default: ${params.kmaindex_nbp}",
+            cliflag: '-nbp',
+            clivalue: (params.kmaindex_nbp ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file