Fix GUI Tasks build warnings

docroot/common_tasks/gui_tasks.rst

@@ -12,7 +12,7 @@ Working with Sequences
 
 
 Assemble a Set of Reads into Contigs
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 PATRIC provides an assembly service that allows you to choose between multiple assemblers,
 using either single-read libraries, paired-end reads, or reads stored online in the
@@ -27,19 +27,19 @@ PATRIC provides an annotation service that constructs a private genome from
 contigs and produces a quality report.  See :doc:`/tutorial/genome_annotation/annotation`
 for instructions on submitting the contigs, and :doc:`/tutorial/genome_quality_report/genome_quality_report`
 to read the quality report.  A sample contigs input file and the resulting job output
-can be seen `here <https://patricbrc.org/workspace/[email protected]/Common.Task.Examples/Annotation>`_.
+can be seen here: `Annotation Sample <https://patricbrc.org/workspace/[email protected]/Common.Task.Examples/Annotation>`_.
 Note that most of the links in the Genome Report will not work because all annotated genomes are private
 to the annotating user.
 
 Extract as Many Complete Genomes as Possible from a Meta-Genomic Sample
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The :doc:`/user_guides/services/metagenome_binning_service` provides this function.  For a tutorial,
 see :doc:`/tutorial/metagenomic_binning/metagenomic_binning`.  Example input files for binning and
-their results can be found `here <https://patricbrc.org/workspace/public/[email protected]/PATRIC%20Workshop/Metagenome%20Binning/ICU%20Metagenome>`_.
+their results can be found here: `Binning Example <https://patricbrc.org/workspace/public/[email protected]/PATRIC%20Workshop/Metagenome%20Binning/ICU%20Metagenome>`_.
 
 Annotate a New Genome and Compare it to Similar Genomes in PATRIC
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 This combines several of the tasks listed elsewhere on this page.  The
 Comprehensive Genome Analysis service takes either reads or contigs and
 creates a private genome integrated into the PATRIC database. It also
@@ -54,7 +54,7 @@ Working with Taxonomic Groups
 -----------------------------
 
 Find Representative Genomes for a Taxon
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 NCBI identifies
 `Reference and Representative genomes for each clade and species <https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/#representative_genomes>`_.
@@ -67,42 +67,42 @@ Instructions for isolating the Reference and Representative genomes are given on
 :ref:`rep-ref-taxon-section`.
 
 Find Genomes in a Taxon with Specific Attributes
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 For the procedure to list the genomes in a taxonomic grouping, see :doc:`/tutorial/searching_and_sorting/genomes_by_taxonomy`.
 Instructions for filtering the list are given on the same page under the heading
 :ref:`taxon-exotic-filtering-section`.
 
 
 Working with Genomes
---------------------
+---------------------
 
 Find the Roles Present in a Genome
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 This is described at :doc:`/tutorial/searching_and_sorting/features_with_roles`.
 
 Compare the Proteomes for a Set of Genomes
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 This is described at :doc:`/tutorial/proteome_comparison/proteome_comparison`.
 
 Visually Compare the Protein Families in a Set of Genomes
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 This is described at :doc:`/tutorial/protein_family_sorter/protein_family_sorter`.  A description of
 the output and how to manipulate it can be found `here <../user_guides/organisms_taxon/protein_families.html#protein-family-sorter-heatmap>`_
 
 Determine the Evidence of Quality for a Genome
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 A quality analysis is performed on every private genome created using :doc:`/tutorial/genome_annotation/annotation`.
 The analysis results are stored
 in a file called *GenomeReport.html* in the annotation service output folder.  A description of how to read this
 file is in the tutorial :doc:`/tutorial/genome_quality_report/genome_quality_report`.
 
 Find the Closest N Genomes to a Particular Genome
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Use the :doc:`/tutorial/similar_genome_finder/similar_genome_finder`.  For more information
 read :doc:`/user_guides/services/similar_genome_finder_service`.
@@ -112,12 +112,12 @@ Working with Protein Families
 -----------------------------
 
 List the Features in a Protein Family and the Genomes Containing Them
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 This procedure is described in :ref:`feature-protein-family-id`.
 
 Find the Function of a Protein Family
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 First, get a list of the features in the protein family using :ref:`feature-protein-family-id`
 or :ref:`feature-protein-family-list`.  Then use the procedure in :ref:`feature-protein-family-function`.
@@ -128,12 +128,12 @@ Working with Features
 
 
 Find the Sequence, Protein Translation, and Other Known Attributes of a Gene
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The many attributes of a feature are displayed on the :doc:`/user_guides/organisms_gene/overview`.
 
 Find the Upstream Region of a Gene
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The upstream region can be seen most clearly using the :doc:`/user_guides/organisms_gene/compare_region_viewer`.  The
 upstream region is shown to the left of the red arrow.
@@ -150,7 +150,7 @@ Create an Alignment and the Associated Phylogenetic Tree from a Set of Features
 This is described in :doc:`/tutorial/alignments/multiple_sequence_alignment`.
 
 Find the Papers Relating to a Specific Feature
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 This information is displayed in the right-hand column of the :doc:`/user_guides/organisms_gene/overview`.