--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.7.0/lib/help/tuspy.nf	Mon Jul 15 10:42:02 2024 -0400
@@ -0,0 +1,78 @@
+// Help text for get_top_unique_mash_hit_genomes.py (tuspy) within CPIPES.
+
+def tuspyHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'tuspy_run': [
+            clihelp: 'Run the get_top_unique_mash_hits_genomes.py ' +
+                'script. Default: ' +
+                (params.tuspy_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'tuspy_s': [
+            clihelp: 'Absolute UNIX path to metadata text file with the ' +
+                'field separator, | and ' +
+                '5 fields: serotype|asm_lvl|asm_url|snp_cluster_id' +
+                'Ex: serotype=Derby,antigen_formula=4:f,g:-|Scaffold|402440|ftp://...' +
+                '|PDS000096654.2. Mentioning this option will create a pickle file for the ' +
+                'provided metadata and exits.' +
+                " Default: ${params.tuspy_s}",
+            cliflag: '-s',
+            clivalue: (params.tuspy_s ?: '')
+        ],
+        'tuspy_m': [
+            clihelp: 'Absolute UNIX path to mash screen results file.' +
+                " Default: ${params.tuspy_m}",
+            cliflag: '-m',
+            clivalue: (params.tuspy_m ?: '')
+        ],
+        'tuspy_ps': [
+            clihelp: 'Absolute UNIX Path to serialized metadata object ' +
+                'in a pickle file.' +
+                " Default: ${params.tuspy_ps}",
+            cliflag: '-ps',
+            clivalue: (params.tuspy_ps ?: '')
+        ],
+        'tuspy_gd': [
+            clihelp: 'Absolute UNIX Path to directory containing ' +
+                'gzipped genome FASTA files.' +
+                " Default: ${params.tuspy_gd}",
+            cliflag: '-gd',
+            clivalue: (params.tuspy_gd ?: '')
+        ],
+        'tuspy_gds': [
+            clihelp: 'Genome FASTA file suffix to search for in the ' +
+                'genome directory.' +
+                " Default: ${params.tuspy_gds}",
+            cliflag: '-gds',
+            clivalue: (params.tuspy_gds ?: '')
+        ],
+        'tuspy_n': [
+            clihelp: 'Return up to this many number of top N unique ' +
+                'genome accession hits.' +
+                " Default: ${params.tuspy_n}",
+            cliflag: '-n',
+            clivalue: (params.tuspy_n ?: '')
+        ],
+        'tuspy_skip': [
+            clihelp: 'Skip all hits which belong to the following bioproject ' +
+                'accession(s). A comma separated list of more than one bioproject. ' +
+                " Default: ${params.tuspy_skip}",
+            cliflag: '-skip',
+            clivalue: (params.tuspy_skip ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
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