--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/kmaalign.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,200 @@
+// Help text for kma align within CPIPES.
+
+def kmaalignHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'kmaalign_run': [
+            clihelp: 'Run kma tool. Default: ' +
+                (params.kmaalign_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'kmaalign_int': [
+            clihelp: 'Input file has interleaved reads. ' +
+                " Default: ${params.kmaalign_int}",
+            cliflag: '-int',
+            clivalue: (params.kmaalign_int ? ' ' : '')
+        ], 
+        'kmaalign_ef': [
+            clihelp: 'Output additional features. ' +
+                "Default: ${params.kmaalign_ef}",
+            cliflag: '-ef',
+            clivalue: (params.kmaalign_ef ? ' ' : '')
+        ], 
+        'kmaalign_vcf': [
+            clihelp: 'Output vcf file. 2 to apply FT. ' +
+                "Default: ${params.kmaalign_vcf}",
+            cliflag: '-vcf',
+            clivalue: (params.kmaalign_vcf ? ' ' : '')
+        ],
+        'kmaalign_sam': [
+            clihelp: 'Output SAM, 4/2096 for mapped/aligned. ' +
+                "Default: ${params.kmaalign_sam}",
+            cliflag: '-sam',
+            clivalue: (params.kmaalign_sam ? ' ' : '')
+        ],
+        'kmaalign_nc': [
+            clihelp: 'No consensus file. ' +
+                "Default: ${params.kmaalign_nc}",
+            cliflag: '-nc',
+            clivalue: (params.kmaalign_nc ? ' ' : '')
+        ],
+        'kmaalign_na': [
+            clihelp: 'No aln file. ' +
+                "Default: ${params.kmaalign_na}",
+            cliflag: '-na',
+            clivalue: (params.kmaalign_na ? ' ' : '')
+        ],
+        'kmaalign_nf': [
+            clihelp: 'No frag file. ' +
+                "Default: ${params.kmaalign_nf}",
+            cliflag: '-nf',
+            clivalue: (params.kmaalign_nf ? ' ' : '')
+        ],
+        'kmaalign_a': [
+            clihelp: 'Output all template mappings. ' +
+                "Default: ${params.kmaalign_a}",
+            cliflag: '-a',
+            clivalue: (params.kmaalign_a ? ' ' : '')
+        ],
+        'kmaalign_and': [
+            clihelp: 'Use both -mrs and p-value on consensus. ' +
+                "Default: ${params.kmaalign_and}",
+            cliflag: '-and',
+            clivalue: (params.kmaalign_and ? ' ' : '')
+        ],
+        'kmaalign_oa': [
+            clihelp: 'Use neither -mrs or p-value on consensus. ' +
+                "Default: ${params.kmaalign_oa}",
+            cliflag: '-oa',
+            clivalue: (params.kmaalign_oa ? ' ' : '')
+        ],
+        'kmaalign_bc': [
+            clihelp: 'Minimum support to call bases. ' +
+                "Default: ${params.kmaalign_bc}",
+            cliflag: '-bc',
+            clivalue: (params.kmaalign_bc ?: '')
+        ],
+        'kmaalign_bcNano': [
+            clihelp: 'Altered indel calling for ONT data. ' +
+                "Default: ${params.kmaalign_bcNano}",
+            cliflag: '-bcNano',
+            clivalue: (params.kmaalign_bcNano ? ' ' : '')
+        ],
+        'kmaalign_bcd': [
+            clihelp: 'Minimum depth to call bases. ' +
+                "Default: ${params.kmaalign_bcd}",
+            cliflag: '-bcd',
+            clivalue: (params.kmaalign_bcd ?: '')
+        ],
+        'kmaalign_bcg': [
+            clihelp: 'Maintain insignificant gaps. ' +
+                "Default: ${params.kmaalign_bcg}",
+            cliflag: '-bcg',
+            clivalue: (params.kmaalign_bcg ? ' ' : '')
+        ],
+        'kmaalign_ID': [
+            clihelp: 'Minimum consensus ID. ' +
+                "Default: ${params.kmaalign_ID}",
+            cliflag: '-ID',
+            clivalue: (params.kmaalign_ID ?: '')
+        ],
+        'kmaalign_md': [
+            clihelp: 'Minimum depth. ' +
+                "Default: ${params.kmaalign_md}",
+            cliflag: '-md',
+            clivalue: (params.kmaalign_md ?: '')
+        ],
+        'kmaalign_dense': [
+            clihelp: 'Skip insertion in consensus. ' +
+                "Default: ${params.kmaalign_dense}",
+            cliflag: '-dense',
+            clivalue: (params.kmaalign_dense ? ' ' : '')
+        ],
+        'kmaalign_ref_fsa': [
+            clihelp: 'Use Ns on indels. ' +
+                "Default: ${params.kmaalign_ref_fsa}",
+            cliflag: '-ref_fsa',
+            clivalue: (params.kmaalign_ref_fsa ? ' ' : '')
+        ],
+        'kmaalign_Mt1': [
+            clihelp: 'Map everything to one template. ' +
+                "Default: ${params.kmaalign_Mt1}",
+            cliflag: '-Mt1',
+            clivalue: (params.kmaalign_Mt1 ? ' ' : '')
+        ],
+        'kmaalign_1t1': [
+            clihelp: 'Map one query to one template. ' +
+                "Default: ${params.kmaalign_1t1}",
+            cliflag: '-1t1',
+            clivalue: (params.kmaalign_1t1 ? ' ' : '')
+        ],
+        'kmaalign_mrs': [
+            clihelp: 'Minimum relative alignment score. ' +
+                "Default: ${params.kmaalign_mrs}",
+            cliflag: '-mrs',
+            clivalue: (params.kmaalign_mrs ?: '')
+        ],
+        'kmaalign_mrc': [
+            clihelp: 'Minimum query coverage. ' +
+                "Default: ${params.kmaalign_mrc}",
+            cliflag: '-mrc',
+            clivalue: (params.kmaalign_mrc ?: '')
+        ],
+        'kmaalign_mp': [
+            clihelp: 'Minimum phred score of trailing and leading bases. ' +
+                "Default: ${params.kmaalign_mp}",
+            cliflag: '-mp',
+            clivalue: (params.kmaalign_mp ?: '')
+        ],
+        'kmaalign_mq': [
+            clihelp: 'Set the minimum mapping quality. ' +
+                "Default: ${params.kmaalign_mq}",
+            cliflag: '-mq',
+            clivalue: (params.kmaalign_mq ?: '')
+        ],
+        'kmaalign_eq': [
+            clihelp: 'Minimum average quality score. ' +
+                "Default: ${params.kmaalign_eq}",
+            cliflag: '-eq',
+            clivalue: (params.kmaalign_eq ?: '')
+        ],
+        'kmaalign_5p': [
+            clihelp: 'Trim 5 prime by this many bases. ' +
+                "Default: ${params.kmaalign_5p}",
+            cliflag: '-5p',
+            clivalue: (params.kmaalign_5p ?: '')
+        ],
+        'kmaalign_3p': [
+            clihelp: 'Trim 3 prime by this many bases ' +
+                "Default: ${params.kmaalign_3p}",
+            cliflag: '-3p',
+            clivalue: (params.kmaalign_3p ?: '')
+        ],
+        'kmaalign_apm': [
+            clihelp: 'Sets both -pm and -fpm ' +
+                "Default: ${params.kmaalign_apm}",
+            cliflag: '-apm',
+            clivalue: (params.kmaalign_apm ?: '')
+        ],
+        'kmaalign_cge': [
+            clihelp: 'Set CGE penalties and rewards ' +
+                "Default: ${params.kmaalign_cge}",
+            cliflag: '-cge',
+            clivalue: (params.kmaalign_cge ? ' ' : '')
+        ],
+
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file