--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/sourmashsearch.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,134 @@
+// Help text for sourmash search within CPIPES.
+
+def sourmashsearchHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'sourmashsearch_run': [
+            clihelp: 'Run `sourmash search` tool. Default: ' +
+                (params.sourmashsearch_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'sourmashsearch_n': [
+            clihelp: 'Number of results to report. ' +
+                'By default, will terminate at --sourmashsearch_thr value. ' +
+                "Default: ${params.sourmashsearch_n}",
+            cliflag: '-n',
+            clivalue: (params.sourmashsearch_n ?: '')
+        ],
+        'sourmashsearch_thr': [
+            clihelp: 'Reporting threshold (similarity) to return results. ' +
+                "Default: ${params.sourmashsearch_thr}",
+            cliflag: '--threshold',
+            clivalue: (params.sourmashsearch_thr ?: '')
+        ],
+        'sourmashsearch_contain': [
+            clihelp: 'Score based on containment rather than similarity. ' +
+                "Default: ${params.sourmashsearch_contain}",
+            cliflag: '--containment',
+            clivalue: (params.sourmashsearch_contain ? ' ' : '')
+        ],
+        'sourmashsearch_maxcontain': [
+            clihelp: 'Score based on max containment rather than similarity. ' +
+                "Default: ${params.sourmashsearch_contain}",
+            cliflag: '--max-containment',
+            clivalue: (params.sourmashsearch_maxcontain ? ' ' : '')
+        ],
+        'sourmashsearch_ignoreabn': [
+            clihelp: 'Do NOT use k-mer abundances if present. ' +
+                "Default: ${params.sourmashsearch_ignoreabn}",
+            cliflag: '--ignore-abundance',
+            clivalue: (params.sourmashsearch_ignoreabn ? ' ' : '')
+        ],
+        'sourmashsearch_ani_ci': [
+            clihelp: 'Output confidence intervals for ANI estimates. ' +
+                "Default: ${params.sourmashsearch_ani_ci}",
+            cliflag: '--estimate-ani-ci',
+            clivalue: (params.sourmashsearch_ani_ci ? ' ' : '')
+        ],
+        'sourmashsearch_k': [
+            clihelp: 'The k-mer size to select. ' +
+                "Default: ${params.sourmashsearch_k}",
+            cliflag: '-k',
+            clivalue: (params.sourmashsearch_k ?: '')
+        ],
+        'sourmashsearch_protein': [
+            clihelp: 'Choose a protein signature. ' +
+                "Default: ${params.sourmashsearch_protein}",
+            cliflag: '--protein',
+            clivalue: (params.sourmashsearch_protein ? ' ' : '')
+        ],
+        'sourmashsearch_noprotein': [
+            clihelp: 'Do not choose a protein signature. ' +
+                "Default: ${params.sourmashsearch_noprotein}",
+            cliflag: '--no-protein',
+            clivalue: (params.sourmashsearch_noprotein ? ' ' : '')
+        ],
+        'sourmashsearch_dayhoff': [
+            clihelp: 'Choose Dayhoff-encoded amino acid signatures. ' +
+                "Default: ${params.sourmashsearch_dayhoff}",
+            cliflag: '--dayhoff',
+            clivalue: (params.sourmashsearch_dayhoff ? ' ' : '')
+        ],
+        'sourmashsearch_nodayhoff': [
+            clihelp: 'Do not choose Dayhoff-encoded amino acid signatures. ' +
+                "Default: ${params.sourmashsearch_nodayhoff}",
+            cliflag: '--no-dayhoff',
+            clivalue: (params.sourmashsearch_nodayhoff ? ' ' : '')
+        ],
+        'sourmashsearch_hp': [
+            clihelp: 'Choose hydrophobic-polar-encoded amino acid signatures. ' +
+                "Default: ${params.sourmashsearch_hp}",
+            cliflag: '--hp',
+            clivalue: (params.sourmashsearch_hp ? ' ' : '')
+        ],
+        'sourmashsearch_nohp': [
+            clihelp: 'Do not choose hydrophobic-polar-encoded amino acid signatures. ' +
+                "Default: ${params.sourmashsearch_nohp}",
+            cliflag: '--no-hp',
+            clivalue: (params.sourmashsearch_nohp ? ' ' : '')
+        ],
+        'sourmashsearch_dna': [
+            clihelp: 'Choose DNA signature. ' +
+                "Default: ${params.sourmashsearch_dna}",
+            cliflag: '--dna',
+            clivalue: (params.sourmashsearch_dna ? ' ' : '')
+        ],
+        'sourmashsearch_nodna': [
+            clihelp: 'Do not choose DNA signature. ' +
+                "Default: ${params.sourmashsearch_nodna}",
+            cliflag: '--no-dna',
+            clivalue: (params.sourmashsearch_nodna ? ' ' : '')
+        ],
+        'sourmashsearch_scaled': [
+            clihelp: 'Scaled value should be between 100 and 1e6. ' +
+                "Default: ${params.sourmashsearch_scaled}",
+            cliflag: '--scaled',
+            clivalue: (params.sourmashsearch_scaled ?: '')
+        ],
+        'sourmashsearch_inc_pat': [
+            clihelp: 'Search only signatures that match this pattern in name, filename, or md5. ' +
+                "Default: ${params.sourmashsearch_inc_pat}",
+            cliflag: '--include-db-pattern',
+            clivalue: (params.sourmashsearch_inc_pat ?: '')
+        ],
+        'sourmashsearch_exc_pat': [
+            clihelp: 'Search only signatures that do not match this pattern in name, filename, or md5. ' +
+                "Default: ${params.sourmashsearch_exc_pat}",
+            cliflag: '--exclude-db-pattern',
+            clivalue: (params.sourmashsearch_exc_pat ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file