--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/lib/help/guncrun.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,92 @@
+// Help text for gunc run within CPIPES.
+
+def guncrunHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'guncrun_run': [
+            clihelp: 'Run `gunc run` tool. Default: ' +
+                (params.guncrun_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'guncrun_in_is_fasta': [
+            clihelp: 'Is input a file in FASTA format. ' +
+                "Default: ${params.guncrun_in_is_fasta}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'guncrun_in_is_fofn': [
+            clihelp: 'Is input a file of file names. ' +
+                "Default: ${params.guncrun_in_is_fofn}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'guncrun_in_is_dir': [
+            clihelp: 'Is input a directory of FASTA files. ' +
+                "Default: ${params.guncrun_in_is_dir}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'guncrun_file_suffix': [
+            clihelp: "Suffix of files if input is a directory. " +
+                "Default: ${params.guncrun_file_suffix}",
+            cliflag: '--file_suffix',
+            clivalue: (params.guncrun_file_suffix ?: '')
+        ],
+        'guncrun_gene_calls': [
+            clihelp: 'Input files are in FASTA faa format. ' +
+                "Default: ${params.guncrun_gene_calls}",
+            cliflag: '--gene_calls',
+            clivalue: (params.guncrun_gene_calls ? ' ' : '')
+        ],
+        'guncrun_temp_dir': [
+            clihelp: 'Path to directory to store temp files. ' +
+                "Default: ${params.guncrun_temp_dir}",
+            cliflag: '--temp_dir',
+            clivalue: (params.guncrun_temp_dir ?: '')
+        ],
+        'guncrun_sensitive': [
+            clihelp: 'Run with high sensitivity. ' +
+                "Default: ${params.guncrun_sensitive}",
+            cliflag: '--sensitive',
+            clivalue: (params.guncrun_sensitive ? ' ' : '')
+        ],
+        'guncrun_detailed_output': [
+            clihelp: 'Output scores for every taxa level. ' +
+                "Default: ${params.guncrun_detailed_output}",
+            cliflag: '--detailed_output',
+            clivalue: (params.guncrun_detailed_output ? ' ' : '')
+        ],
+        'guncrun_ctg_tax_output': [
+            clihelp: 'Output assignments for each contig. ' +
+                "Default: ${params.guncrun_ctg_tax_output}",
+            cliflag: '--contig_taxonomy_output',
+            clivalue: (params.guncrun_ctg_tax_output ? ' ' : '')
+        ],
+        'guncrun_use_species_lvl': [
+            clihelp: 'Allow species level to be picked as maxCSS. ' +
+                "Default: ${params.guncrun_use_species_lvl}",
+            cliflag: '--use_species_level',
+            clivalue: (params.guncrun_use_species_lvl ? ' ' : '')
+        ],
+        'guncrun_min_mapped_genes': [
+            clihelp: 'Do not calculate GUNC score if number of mapped ' +
+                'genes is below this value. ' +
+                "Default: ${params.guncrun_min_mapped_genes}",
+            cliflag: '--min_mapped_genes',
+            clivalue: (params.guncrun_min_mapped_genes ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file