--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/lib/help/checkm2predict.nf	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,99 @@
+// Help text for checkm2 predict within CPIPES.
+
+def checkm2predictHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'checkm2predict_run': [
+            clihelp: 'Run `checkm2 predict` tool. Default: ' +
+                (params.checkm2predict_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'checkm2predict_quiet': [
+            clihelp: 'Only output errors. ' +
+                "Default: ${params.checkm2predict_quiet}",
+            cliflag: '--quiet',
+            clivalue: (params.checkm2predict_quiet ? ' ' : '')
+        ],
+        'checkm2predict_lowmem': [
+            clihelp: 'Low memory mode. Reduces DIAMOND blocksize to ' +
+                'significantly reduce RAM usage at the expense of longer runtime. ' +
+                "Default: ${params.checkm2predict_lowmem}",
+            cliflag: '--lowmem',
+            clivalue: (params.checkm2predict_lowmem ? ' ' : '')
+        ],
+        'checkm2predict_general': [
+            clihelp: 'Force the use of the general quality prediction model (gradient boost). ' +
+                "Default: ${params.checkm2predict_general}",
+            cliflag: '--general',
+            clivalue: (params.checkm2predict_general ? ' ' : '')
+        ],
+        'checkm2predict_specific': [
+            clihelp: "Force the use of the specific quality prediction model (neural network) " +
+                "Default: ${params.checkm2predict_specific}",
+            cliflag: '--specific',
+            clivalue: (params.checkm2predict_specific ? ' ' : '')
+        ],
+        'checkm2predict_allmodels': [
+            clihelp: 'Output quality prediction for both models for each genome. ' +
+                "Default: ${params.checkm2predict_allmodels}",
+            cliflag: '--allmodels',
+            clivalue: (params.checkm2predict_allmodels ? ' ' : '')
+        ],
+        'checkm2predict_genes': [
+            clihelp: 'Treat input files as protein files. ' +
+                "Default: ${params.checkm2predict_genes}",
+            cliflag: '--genes',
+            clivalue: (params.checkm2predict_genes ? ' ' : '')
+        ],
+        'checkm2predict_x': [
+            clihelp: 'Extension of input files. ' +
+                "Default: ${params.checkm2predict_x}",
+            cliflag: '-x',
+            clivalue: (params.checkm2predict_x ?: '')
+        ],
+        'checkm2predict_tmpdir': [
+            clihelp: 'Specify an alternate directory for temporary files. ' +
+                "Default: ${params.checkm2predict_tmpdir}",
+            cliflag: '--tmpdir',
+            clivalue: (params.checkm2predict_tmpdir ?: '')
+        ],
+        'checkm2predict_rminterfiles': [
+            clihelp: 'Remove all intermediate files (protein files, diamond output). ' +
+                "Default: ${params.checkm2predict_rminterfiles}",
+            cliflag: '--remove_intermediates',
+            clivalue: (params.checkm2predict_rminterfiles ? ' ' : '')
+        ],
+        'checkm2predict_ttable': [
+            clihelp: 'Provide a specific progidal translation table for bins. The default ' +
+                'value of false will automatically determine either 11 or 4. ' +
+                "Default: ${params.checkm2predict_ttable}",
+            cliflag: '--ttable',
+            clivalue: (params.checkm2predict_ttable ? ' ' : '')
+        ],
+        'checkm2predict_dbg_cos': [
+            clihelp: 'DEBUG: Write cosine similarity values to a file. ' +
+                "Default: ${params.checkm2predict_dbg_cos}",
+            cliflag: '--dbg_cos',
+            clivalue: (params.checkm2predict_dbg_cos ? ' ' : '')
+        ],
+        'checkm2predict_dbg_vectors': [
+            clihelp: 'DEBUG: Write Dump pickled feature vectors to a file. ' +
+                "Default: ${params.checkm2predict_dbg_vectors}",
+            cliflag: '--dbg_vectors',
+            clivalue: (params.checkm2predict_dbg_vectors ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file