Add --no_shed_install option.

docs/test_format.rst

@@ -33,9 +33,9 @@ same testing file format is used for both kinds of artifacts.
       job: pear_job.yml
       outputs:
         assembled_pairs:
-          file: test-data/pear_assembled_results1.fastq
+          path: test-data/pear_assembled_results1.fastq
         unassembled_forward_reads:
-          file: test-data/pear_unassembled_forward_results1.fastq
+          path: test-data/pear_unassembled_forward_results1.fastq
 
 
 .. code-block:: yaml
@@ -50,13 +50,13 @@ same testing file format is used for both kinds of artifacts.
           path: mutant_R2.fastq
         wildtype.fna:
           class: File
-          path: wildtype.fna
+          location: https://zenodo.org/record/582600/files/wildtype.fna
         wildtype.gbk:
           class: File
-          path: wildtype.gbk
+          location: https://zenodo.org/record/582600/files/wildtype.gbk
         wildtype.gff:
           class: File
-          path: wildtype.gff
+          location: https://zenodo.org/record/582600/files/wildtype.gff
       outputs:
         jbrowse_html:
           asserts:
@@ -85,6 +85,11 @@ The job input file is a proper CWL_ job document - which is fairly straight forw
 the above examples. Planemo adapts the CWL_ job document to Galaxy_ workflows and tools - using input
 names for Galaxy_ tools and input node labels for workflows.
 
+Input files can be specified using either ``path`` attributes (which should generally be file
+paths relative to the aritfact and test directory) or ``location`` (which should be a URI). The 
+examples above demonstrate using both paths relative to the tool file and test data published
+to `Zenodo <https://zenodo.org/>`__.
+
 .. note::
 
     These job objects can be run directly with ``planemo run``.
@@ -241,11 +246,13 @@ option to mount test data into the testing container.
 ``external_galaxy``
 ~~~~~~~~~~~~~~~~~~~~
 
-    $ planemo test --engine external_galaxy --galaxy_admin_key <admin_key> --galaxy_user_key <user_key> --galaxy_user <url>
+    $ planemo test --engine external_galaxy --galaxy_admin_key <admin_key> --galaxy_user_key <user_key> [--no_shed_install] <url>
 
 This is primarily useful for testing workflows against already running Galaxy instances. An admin or
 master API key should be supplied to install missing tool repositories for the workflow and a user API
-key should be supplied to run the workflow using.
+key should be supplied to run the workflow using. If you wish to skip tool shed repository installation
+(this requires the tool all be present already), use the ``-no_shed_install`` option with the ``test``
+command.
 
 To run tool tests against a running Galaxy, ``galaxy-tool-test`` is a script that gets installed with 
 galaxy-lib and so may very well already be on your ``PATH``. Check out the options available with that

planemo/galaxy/config.py

@@ -741,7 +741,9 @@ def install_workflows(self):
                 self._install_workflow(runnable)
 
     def _install_workflow(self, runnable):
-        install_shed_repos(runnable, self.gi, self._kwds.get("ignore_dependency_problems", False))
+        if self._kwds["shed_install"]:
+            install_shed_repos(runnable, self.gi, self._kwds.get("ignore_dependency_problems", False))
+
         # TODO: Allow serialization so this doesn't need to assume a
         # shared filesystem with Galaxy server.
         from_path = runnable.type.name == "cwl_workflow"

planemo/options.py

@@ -607,6 +607,17 @@ def paste_test_data_paths_option():
     )
 
 
+def shed_install_option():
+    return planemo_option(
+        "--shed_install/--no_shed_install",
+        is_flag=True,
+        default=True,
+        help=("By default Planemo will attempt to install repositories needed for workflow "
+              "testing. This may not be appropriate for production servers and so this can "
+              "disabled by calling planemo with --no_shed_install.")
+    )
+
+
 def single_user_mode_option():
     return planemo_option(
         "galaxy_single_user",
@@ -1108,6 +1119,7 @@ def galaxy_serve_options():
         daemon_option(),
         pid_file_option(),
         ignore_dependency_problems_option(),
+        shed_install_option()
     )
 
 
@@ -1203,6 +1215,7 @@ def engine_options():
         docker_galaxy_image_option(),
         docker_extra_volume_option(),
         ignore_dependency_problems_option(),
+        shed_install_option(),
         galaxy_url_option(),
         galaxy_admin_key_option(),
         galaxy_user_key_option(),