Doc and option improvements.

- Fix link in Conda docs.
- Allow --biocontainers as an option to lint and test in lieu of (--biocontainer and --mulled_container respectively).

Author: jmchilton

docs/_writing_dependencies_conda.rst

@@ -248,7 +248,7 @@ all the software and all the versions available matching that search term - incl
 
 Alternatively the Anaconda_ website can be used to search for packages. Typing ``seqtk``
 into the search form on that page and clicking the top result will bring on to `this page
-https://anaconda.org/bioconda/seqtk`__ with information about the Bioconda package.
+<https://anaconda.org/bioconda/seqtk>`__ with information about the Bioconda package.
 
 When using the website to search though, you need to aware of what channel you are using. By
 default, Planemo and Galaxy will search a few different Conda channels. While it is possible

docs/_writing_dependencies_docker.rst

@@ -47,7 +47,7 @@ tool from the introductory tutorial.
 
 ::
 
-    $ planemo lint --biocontainer seqtk_xml
+    $ planemo lint --biocontainers seqtk_seq.xml
     Linting tool /home/planemo/workspace/planemo/project_templates/seqtk_complete/seqtk_seq.xml
     Applying linter tests... CHECK
     .. CHECK: 1 test(s) found.
@@ -83,7 +83,7 @@ Docker container using the flag ``--mulled_containers`` as shown (in part) next.
 
 ::
 
-    $ planemo test --mulled_containers seqtk_seq.xml
+    $ planemo test --biocontainers seqtk_seq.xml
     ...
     2017-03-01 08:18:19,669 INFO  [galaxy.tools.actions] Handled output named output1 for tool seqtk_seq (22.145 ms)
     2017-03-01 08:18:19,683 INFO  [galaxy.tools.actions] Added output datasets to history (14.604 ms)

planemo/commands/cmd_lint.py

@@ -34,7 +34,9 @@
     help="Check tool requirements for availability in best practice Conda channels.",
 )
 @click.option(
+    "biocontainer",
     "--biocontainer",
+    "--biocontainers",
     is_flag=True,
     default=False,
     help="Check best practice BioContainer namespaces for a container definition applicable for this tool.",

planemo/options.py

@@ -343,7 +343,9 @@ def job_config_option():
 
 def mulled_containers_option():
     return planemo_option(
+        "mulled_containers",
         "--mulled_containers",
+        "--biocontainers",
         is_flag=True,
         help="Test tools against mulled containers (forces --docker).",
     )