adding docs

.gitignore

@@ -1 +1,2 @@
 test
+docs/_site

docs/.on-save.json

@@ -0,0 +1,7 @@
+[
+  {
+    "files": ["*/*", "*"],
+    "command": "conda run -n base sphinx-build . _site",
+    "showOutput": "false"
+  }
+]

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/style.css

@@ -0,0 +1,6 @@
+.wy-nav-content {
+    max-width: 100% !important;
+}
+p {
+     text-align:justify;
+}

docs/conf.py

@@ -0,0 +1,85 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Easy (minimal) circos plot.'
+copyright = '2021, Felipe, Almeida. Easy_circos: Simple script to create a circos plot between FASTA files'
+author = 'Felipe Marques de Almeida'
+
+
+# -- General configuration ---------------------------------------------------
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx_copybutton"
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+
+# --- default ---
+#import sphinx_rtd_theme
+#html_theme = 'sphinx_rtd_theme'
+
+# --- material ---
+#import sphinx_materialdesign_theme
+#html_theme = "sphinx_materialdesign_theme"
+
+# --- jupyter ---
+#import jupyter_sphinx_theme
+#html_theme = "jupyter"
+#html_sidebars = {'**': ['sidebartoc.html']}
+#html_theme_path = jupyter_sphinx_theme.get_html_theme_path()
+
+# --- karma ---
+html_theme = "karma_sphinx_theme"
+
+# --- custom css ---
+html_title       = project
+html_static_path = ['_static']
+html_css_files   = ['style.css']
+
+# Copy button configuration --------------------------------------------------
+# Source: https://sphinx-copybutton.readthedocs.io/en/latest/
+#copybutton_prompt_text = "$ "

docs/index.rst

@@ -0,0 +1,38 @@
+.. _index:
+
+easy_circos
+===========
+
+`Easy_circos <https://github.com/fmalmeida/easy_circos>`_ is a simple `conda <https://conda.io/>`_ package that aims on rapidly and easily creating minimal circos configurations templates based on input data so that users can further customize and plot by their own desires.
+
+Installation
+""""""""""""
+
+Installation is described in the `github main page <https://github.com/fmalmeida/easy_circos>`_.
+
+Available features
+""""""""""""""""""
+
+For now, it can create a circos plot with:
+
+* Chromosome Ideograms. See `circos manual ideograms <http://circos.ca/documentation/tutorials/ideograms/ideograms/lesson>`_.
+* Tick marks of chr lengths. See `circos manual ticks <http://circos.ca/documentation/tutorials/ticks_and_labels/basics/>`_.
+* GC Skew plot.
+* Tiles and text labels from 2D tracks. Eg. genomic regions. See `circos manual 2D tracks <http://circos.ca/documentation/tutorials/2d_tracks/>`_.
+* Similarity links between one or more FASTAs. See `circos manual links <http://circos.ca/documentation/tutorials/links/>`_.
+
+.. toctree::
+   :hidden:
+   :caption: Kickoff
+
+   quickstart
+
+.. toctree::
+   :hidden:
+   :caption: Reference book
+
+   manual
+
+Support Contact
+===============
+Whenever a doubt arise feel free to contact me at almeidafmarques@gmail.com

docs/manual.rst

@@ -0,0 +1,139 @@
+.. _manual:
+
+Manual
+======
+
+.. code-block:: bash
+
+  # Get help in the command line
+  nextflow run fmalmeida/bacannot-compare --help
+
+Input files
+-----------
+
+This toolkit takes as input a directory containing the results obtained with the `bacannot pipeline <https://github.com/fmalmeida/bacannot>`_ (generally, the ``--outdir`` parameter).
+
+.. warning::
+
+	**This toolkit requires that at least two genome annotations are available.**
+
+.. tip::
+
+	As described in `the bacannot manual <https://bacannot.readthedocs.io/en/latest/outputs.html>`_, each genome annotation will (or must be) be placed in an individual subdirectory inside the main directory. This subdirectories are generally named with the genome prefixes or the ``--prefix`` parameter.
+
+.. list-table::
+   :widths: 20 10 20 30
+   :header-rows: 1
+
+   * - Arguments
+     - Required
+     - Default value
+     - Description
+
+   * - ``--dir``
+     - Y
+     - NA
+     - Path to the directory containing the annotation results of the bacannot pipeline.
+
+Output files
+------------
+
+.. list-table::
+   :widths: 20 10 20 30
+   :header-rows: 1
+
+   * - Arguments
+     - Required
+     - Default value
+     - Description
+
+   * - ``--outdir``
+     - N
+     - By default, they will be placed inside the bacannot main annotation dir.
+     - Path to the directory to place the analyses results.
+
+   * - ``--prefix``
+     - N
+     - BAC-COMPARE-"${DATE}"
+     - The name of the output directory. The results dir will be placed inside the ``--outdir``.
+
+   * - ``--force``
+     - N
+     - False
+     - Force the results to be overwritten when resuming an execution (with ``-resume``). Otherwise, whenever available, nextflow will use the existing results.
+
+Workflow options
+----------------
+
+.. list-table::
+   :widths: 20 10 10 50
+   :header-rows: 1
+
+   * - Arguments
+     - Required
+     - Default value
+     - Description
+
+   * - ``--threads``
+     - N
+     - 2
+     - Set the number of threads to be used by the software.
+
+   * - ``--parallel_jobs``
+     - N
+     - 1
+     - Number of jobs to run in parallel. Each job can consume up to N threads (--threads). Default: 1.
+
+   * - ``--all``
+     - N
+     - False
+     - Activates all analyses.
+
+   * - ``--prokka``
+     - N
+     - False
+     - Activates prokka annotation comparison with multiqc.
+
+   * - ``--pangenome``
+     - N
+     - False
+     - Activates the pangenome estimation using roary.
+
+   * - ``--decoder``
+     - N
+     - False
+     - Activates the KEGG KO annotation comparison with keggdecoder.
+
+   * - ``--phylogeny``
+     - N
+     - False
+     - Activates the phylogeny estimation using parsnp.
+
+   * - ``--resistance``
+     - N
+     - False
+     - Activates the AMR annotation comparison.
+
+   * - ``--kleborate``
+     - N
+     - False
+     - Activates Kleborate/Kaptive analysis (*Klebsiella* genomes).
+
+BlastFrost option
+-----------------
+
+This optinal process uses a nucleotide fasta file to query the genomes and produce a presence/absence matrix, as well as a Heatmap of the hits.
+
+.. list-table::
+   :widths: 20 10 20 30
+   :header-rows: 1
+
+   * - Arguments
+     - Required
+     - Default value
+     - Description
+
+   * - ``--blastfrost_query``
+     - N
+     - NA
+     - A nucleotide fasta file containing a list of query genes to be searched in the genomes.

docs/quickstart.rst

@@ -0,0 +1,72 @@
+.. _quickstart:
+
+Quickstart
+==========
+
+Minimal example
+---------------
+
+Get the data
+""""""""""""
+
+To keep things simple and reproducible, let's work with the reference *E. coli* genomes `K12 <https://www.ncbi.nlm.nih.gov/genome?LinkName=nuccore_genome&from_uid=545778205>`_ and `Sakai <https://www.ncbi.nlm.nih.gov/assembly/GCF_000008865.2>`_:
+
+.. code-block:: bash
+
+   ## download ecoli genome Sakai
+   wget \
+    https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.2_ASM886v2/GCF_000008865.2_ASM886v2_genomic.fna.gz \
+    -O ecoli_sakai.fna.gz && \
+   gzip -d ecoli_sakai.fna.gz
+
+   ## download ecoli genome K12
+   wget \
+    https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz \
+    -O ecoli_k12.fna.gz && \
+  gzip -d ecoli_k12.fna.gz
+
+Prepare input
+"""""""""""""
+
+Before running the script, we must prepare the CSV that is used as input. This CSV must have:
+
+* <FASTA PATH>,<PREFIX>,<COLOR>
+
+We can prepare this csv with:
+
+.. code-block:: bash
+
+   echo "ecoli_k12.fna,K12,purple" > input.fofn
+   echo "ecoli_sakai.fna,SAKAI,lorange" >> input.fofn
+
+The file must look like this (input.fofn):
+
+.. code-block:: bash
+
+   ecoli_k12.fna,K12,purple
+   ecoli_sakai.fna,SAKAI,lorange
+
+Create the circos plot
+""""""""""""""""""""""
+
+With that, we can finally create a minimal circos configuration file and plots having:
+
+* Ideograms
+* Tick marks
+* GC Skew
+* Similarity links
+
+.. code-block:: bash
+
+   plot_circos --fofn input.fofn
+
+This will create all the circos configuration files and required data files under the ``results`` folder (Can be changed with ``--outdir``). See the created plot:
+
+
+
+.. note::
+
+   Under the ``results/conf`` file you will have all the circos configuration plots. With that, you can further customize and increment the plot as you desire. For that, you must understand circos conf files. `See their manual <http://circos.ca/documentation/tutorials/configuration/configuration_files/>`_
+
+Example with 2D tracks
+----------------------

docs/requirements.txt

@@ -0,0 +1,11 @@
+Sphinx==2.2.1
+sphinxcontrib-applehelp==1.0.1
+sphinxcontrib-devhelp==1.0.1
+sphinxcontrib-htmlhelp==1.0.2
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.2
+sphinxcontrib-serializinghtml==1.1.3
+sphinx_materialdesign_theme
+jupyter-sphinx-theme
+karma_sphinx_theme
+sphinx-copybutton

recipe/src/help.sh

@@ -2,7 +2,7 @@ Help()
 {
 cat << EOF
 
-Simple script to create a circos plot between two FASTA files.
+Simple script to create a circos plot between FASTA files.
 Copyright, Felipe Almeida <almeidafmarques@outlook.com>, 2021
 
  Syntax: