--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/lib/help/mashtree.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,81 @@
+// Help text for mashtree within CPIPES.
+
+def mashtreeHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'mashtree_run': [
+            clihelp: 'Run mashtree tool. Default: ' +
+                (params.mashtree_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'mashtree_fofn': [
+            clihelp: 'Input is a file of file names. ' +
+                "Default: ${params.mashtree_fofn}",
+            cliflag: '--file-of-files',
+            clivalue: (params.mashtree_fofn ? ' ' : '')
+        ],
+        'mashtree_trunclength': [
+            clihelp: 'How many characters to keep in filename. ' +
+                "Default: ${params.mashtree_trunclength}",
+            cliflag: '--truncLength',
+            clivalue: (params.mashtree_trunclength ?: '')
+        ],
+        'mashtree_mindepth': [
+            clihelp: 'If mindepth is zero, then it will be chosen in a smart but slower method, ' +
+                'to discard lower-abundance kmers. ' +
+                "Default: ${params.mashtree_mindepth}",
+            cliflag: '--mindepth',
+            clivalue: (params.mashtree_mindepth ?: '')
+        ],
+        'mashtree_kmerlength': [
+            clihelp: "The minimum k-mer length. " +
+                "Default: ${params.mashtree_kmerlength}",
+            cliflag: '--kmerlength',
+            clivalue: (params.mashtree_kmerlength ?: '')
+        ],
+        'mashtree_sketchsize': [
+            clihelp: "The minimum `mash` sketch size. " +
+                "Default: ${params.mashtree_sketchsize}",
+            cliflag: '--sketchsize',
+            clivalue: (params.mashtree_sketchsize ?: '')
+        ],
+        'mashtree_seed': [
+            clihelp: "Seed for `mash` sketch. " +
+                "Default: ${params.mashtree_seed}",
+            cliflag: '--seed',
+            clivalue: (params.mashtree_seed ? ' ' : '')
+        ],
+        'mashtree_genomesize': [
+            clihelp: 'Define genome size. ' +
+                "Default: ${params.mashtree_genomesize}",
+            cliflag: '--genomesize',
+            clivalue: (params.mashtree_genomesize ?: '')
+        ],
+        'mashtree_sigfigs': [
+            clihelp: "How many decimal places to use in mash distances. " +
+                "Default: ${params.mashtree_sigfigs}",
+            cliflag: '--sigfigs',
+            clivalue: (params.mashtree_sigfigs ?: '')
+        ],
+        'mashtree_sortorder': [
+            clihelp: 'For neighbor-joining, the sort order can make a difference. ' +
+                'Options include: ABC (alphabetical), random, input-order. ' +
+                "Default: ${params.mashtree_sortorder}",
+            cliflag: '--sort-order',
+            clivalue: (params.mashtree_sortorder ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file