--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.6.1/lib/help/spades.nf	Tue Sep 05 11:51:40 2023 -0400
@@ -0,0 +1,121 @@
+// Help text for spades within CPIPES.
+
+def spadesHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'spades_run': [
+            clihelp: 'Run SPAdes assembler. Default: ' +
+                (params.spades_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'spades_isolate': [
+            clihelp: 'This flag is highly recommended for high-coverage isolate and ' +
+                "multi-cell data. Default: ${params.spades_isolate}",
+            cliflag: '--isolate',
+            clivalue: (params.spades_isolate ? ' ' : '')
+        ], 
+        'spades_sc': [
+            clihelp: 'This flag is required for MDA (single-cell) data. ' +
+                "Default: ${params.spades_sc}",
+            cliflag: '--sc',
+            clivalue: (params.spades_sc ? ' ' : '')
+        ],
+        'spades_meta': [
+            clihelp: 'This flag is required for metagenomic data. ' +
+                "Default: ${params.spades_meta}",
+            cliflag: '--meta',
+            clivalue: (params.spades_meta ? ' ' : '')
+        ],
+        'spades_bio': [
+            clihelp: 'This flag is required for biosytheticSPAdes mode. ' +
+                "Default: ${params.spades_bio}",
+            cliflag: '--bio',
+            clivalue: (params.spades_bio ? ' ' : '')
+        ],
+        'spades_corona': [
+            clihelp: 'This flag is required for coronaSPAdes mode. ' +
+                "Default: ${params.spades_corona}",
+            cliflag: '--corona',
+            clivalue: (params.spades_corona ? ' ' : '')
+        ],
+        'spades_rna': [
+            clihelp: 'This flag is required for RNA-Seq data. ' +
+                "Default: ${params.spades_rna}",
+            cliflag: '--rna',
+            clivalue: (params.spades_rna ? ' ' : '')
+        ],
+        'spades_plasmid': [
+            clihelp: 'Runs plasmidSPAdes pipeline for plasmid detection. ' +
+                "Default: ${params.spades_plasmid}",
+            cliflag: '--plasmid',
+            clivalue: (params.spades_plasmid ? ' ' : '')
+        ],
+        'spades_metaviral': [
+            clihelp: 'Runs metaviralSPAdes pipeline for virus detection. ' +
+                "Default: ${params.spades_metaviral}",
+            cliflag: '--metaviral',
+            clivalue: (params.spades_metaviral ? ' ' : '')
+        ],
+        'spades_metaplasmid': [
+            clihelp: 'Runs metaplasmidSPAdes pipeline for plasmid detection in ' +
+                "metagenomics datasets. Default: ${params.spades_metaplasmid}",
+            cliflag: '--metaplasmid',
+            clivalue: (params.spades_metaplasmid ? ' ' : '')
+        ],
+        'spades_rnaviral': [
+            clihelp: 'This flag enables virus assembly module from RNA-Seq data. ' +
+                "Default: ${params.spades_rnaviral}",
+            cliflag: '--rnaviral',
+            clivalue: (params.spades_rnaviral ? ' ' : '')
+        ],
+        'spades_iontorrent': [
+            clihelp: 'This flag is required for IonTorrent data. ' +
+                "Default: ${params.spades_iontorrent}",
+            cliflag: '--iontorrent',
+            clivalue: (params.spades_iontorrent ? ' ' : '')
+        ],
+        'spades_only_assembler': [
+            clihelp: 'Runs only the SPAdes assembler module (without read error correction). ' +
+                "Default: ${params.spades_only_assembler}",
+            cliflag: '--only-assembler',
+            clivalue: (params.spades_only_assembler ? ' ' : '')
+        ],
+        'spades_careful': [
+            clihelp: 'Tries to reduce the number of mismatches and short indels in the assembly. ' +
+                "Default: ${params.spades_careful}",
+            cliflag: '--careful',
+            clivalue: (params.spades_careful ? ' ' : '')
+        ],
+        'spades_cov_cutoff': [
+            clihelp: 'Coverage cutoff value (a positive float number). ' +
+                "Default: ${params.spades_cov_cutoff}",
+            cliflag: '--cov-cutoff',
+            clivalue: (params.spades_cov_cutoff ?: '')
+        ],
+        'spades_k': [
+            clihelp: 'List of k-mer sizes (must be odd and less than 128). ' +
+                "Default: ${params.spades_k}",
+            cliflag: '-k',
+            clivalue: (params.spades_k ?: '')
+        ],
+        'spades_hmm': [
+            clihelp: 'Directory with custom hmms that replace the default ones (very rare). ' +
+                "Default: ${params.spades_hmm}",
+            cliflag: '--custom-hmms',
+            clivalue: (params.spades_hmm ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file