--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/seqkitgrep.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,69 @@
+// Help text for seqkit grep within CPIPES.
+
+def seqkitgrepHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'seqkit_grep_n': [
+            clihelp: 'Match by full name instead of just ID. ' +
+                "Default: " + (params.seqkit_grep_n ?: 'undefined'),
+            cliflag: '--seqkit_grep_n',
+            clivalue: (params.seqkit_grep_n ? ' ' : '')
+        ], 
+        'seqkit_grep_s': [
+            clihelp: 'Search subseq on seq, both positive and negative ' +
+                'strand are searched, and mismatch allowed using flag --seqkit_grep_m. ' +
+                "Default: " + (params.seqkit_grep_s ?: 'undefined'),
+            cliflag: '--seqkit_grep_s',
+            clivalue: (params.seqkit_grep_s ? ' ' : '')
+        ],
+        'seqkit_grep_c': [
+            clihelp: 'Input is circular genome ' +
+                "Default: " + (params.seqkit_grep_c ?: 'undefined'),
+            cliflag: '--seqkit_grep_c',
+            clivalue: (params.seqkit_grep_c ? ' ' : '')
+        ],
+        'seqkit_grep_C': [
+            clihelp: 'Just print a count of matching records. With the ' +
+                '--seqkit_grep_v flag, count non-matching records. ' +
+                "Default: " + (params.seqkit_grep_v ?: 'undefined'),
+            cliflag: '--seqkit_grep_v',
+            clivalue: (params.seqkit_grep_v ? ' ' : '')
+        ],
+        'seqkit_grep_i': [
+            clihelp: 'Ignore case while using seqkit grep. ' +
+                "Default: " + (params.seqkit_grep_i ?: 'undefined'),
+            cliflag: '--seqkit_grep_i',
+            clivalue: (params.seqkit_grep_i ? ' ' : '')
+        ],
+        'seqkit_grep_v': [
+            clihelp: 'Invert the match i.e. select non-matching records. ' +
+                "Default: " + (params.seqkit_grep_v ?: 'undefined'),
+            cliflag: '--seqkit_grep_v',
+            clivalue: (params.seqkit_grep_v ? ' ' : '')
+        ],
+        'seqkit_grep_m': [
+            clihelp: 'Maximum mismatches when matching by sequence. ' +
+                "Default: " + (params.seqkit_grep_m ?: 'undefined'),
+            cliflag: '--seqkit_grep_m',
+            clivalue: (params.seqkit_grep_v ?: '')
+        ],
+        'seqkit_grep_r': [
+            clihelp: 'Input patters are regular expressions. ' +
+                "Default: " + (params.seqkit_grep_m ?: 'undefined'),
+            cliflag: '--seqkit_grep_m',
+            clivalue: (params.seqkit_grep_v ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
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