Merge pull request #415 from uclahs-cds/czhu-fix-docs

Documentation fixed for encodeFasta, mergeFasta, decoyFasta and parseArriba
uclahs-cds · Feb 25, 2022 · 830cd37 · 830cd37
2 parents 4a92e42 + 575282e
commit 830cd37
Show file tree

Hide file tree

Showing 5 changed files with 35 additions and 2 deletions.
diff --git a/docs/img/graphic-abstract.png b/docs/img/graphic-abstract.png
diff --git a/docs/parse-arriba.md b/docs/parse-arriba.md
@@ -0,0 +1,24 @@
+{% set command = 'parseArriba' %}
+# {{ command }}
+
+::: moPepGen.cli.parse_arriba
+	handler: python
+    selection:
+      members: false
+    rendering:
+      show_root_heading: false
+      show_source: false
+
+{% include 'partials/_caution_on_reference_version.md' %}
+
+## Usage
+
+```
+{{ get_arg_usage(command) }}
+```
+
+## Arguments
+
+{% with actions=get_arg_data(command) %}
+{% include 'partials/_command_usage.md' %}
+{% endwith %}
diff --git a/main.py b/main.py
@@ -11,12 +11,16 @@
     'parseREDItools': cli.add_subparser_parse_reditools,
     'parseSTARFusion': cli.add_subparser_parse_star_fusion,
     'parseFusionCatcher': cli.add_subparser_parse_fusion_catcher,
+    'parseArriba': cli.add_subparser_parse_arriba,
     'parseRMATS': cli.add_subparser_parse_rmats,
     'parseCIRCexplorer': cli.add_subparser_parse_circexplorer,
     'callVariant': cli.add_subparser_call_variant,
     'callNoncoding': cli.add_subparser_call_noncoding,
     'filterFasta': cli.add_subparser_filter_fasta,
-    'splitDatabase': cli.add_subparser_split_fasta
+    'splitFasta': cli.add_subparser_split_fasta,
+    'mergeFasta': cli.add_subparser_merge_fasta,
+    'encodeFasta': cli.add_subparser_encode_fasta,
+    'decoyFasta': cli.add_subparser_decoy_fasta
 }
 
 def define_env(env):

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -14,12 +14,16 @@ nav:
       - parseREDItools: parse-reditools.md
       - parseSTARFuion: parse-star-fusion.md
       - parseFusionCatcher: parse-fusion-catcher.md
+      - parseArriba: parse-arriba.md
       - parseRMATS: parse-rmats.md
       - parseCIRCexplorer: parse-circexplorer.md
       - callVariant: call-variant.md
       - callNoncoding: call-noncoding.md
       - filterFasta: filter-fasta.md
-      - splitDatabase: split-database.md
+      - splitFasta: split-fasta.md
+      - mergeFasta: merge-fasta.md
+      - encodeFasta: encode-fasta.md
+      - decoyFasta: decoy-fasta.md
 theme: readthedocs
 plugins:
   - mkdocstrings:

diff --git a/moPepGen/cli/decoy_fasta.py b/moPepGen/cli/decoy_fasta.py
@@ -92,6 +92,7 @@ def add_subparser_decoy_fasta(subparser:argparse._SubParsersAction):
     common.add_args_quiet(parser)
     common.print_help_if_missing_args(parser)
     parser.set_defaults(func=decoy_fasta)
+    return parser
 
 class _Summary():
     """ Summary """