Improve command help.

docs/commands.rst

@@ -7,12 +7,19 @@ implemented as a subcommand of the ``planemo`` executable. This section of the
 documentation describes these commands.
 
 
+.. include:: commands/bioc_conda_recipe_init.rst
+.. include:: commands/bioc_tool_init.rst
 .. include:: commands/brew.rst
 .. include:: commands/brew_env.rst
 .. include:: commands/brew_init.rst
+.. include:: commands/ci_find_repos.rst
+.. include:: commands/ci_find_tools.rst
+.. include:: commands/clone.rst
 .. include:: commands/conda_env.rst
 .. include:: commands/conda_init.rst
 .. include:: commands/conda_install.rst
+.. include:: commands/conda_lint.rst
+.. include:: commands/conda_search.rst
 .. include:: commands/config_init.rst
 .. include:: commands/cwl_script.rst
 .. include:: commands/database_create.rst
@@ -23,11 +30,13 @@ documentation describes these commands.
 .. include:: commands/docker_shell.rst
 .. include:: commands/docs.rst
 .. include:: commands/lint.rst
+.. include:: commands/mull.rst
 .. include:: commands/normalize.rst
 .. include:: commands/profile_create.rst
 .. include:: commands/profile_delete.rst
 .. include:: commands/profile_list.rst
 .. include:: commands/project_init.rst
+.. include:: commands/pull_request.rst
 .. include:: commands/run.rst
 .. include:: commands/serve.rst
 .. include:: commands/share_test.rst

docs/commands/bioc_conda_recipe_init.rst

@@ -0,0 +1,31 @@
+
+``bioc_conda_recipe_init`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``bioc_conda_recipe_init``. This help message can be generated with ``planemo bioc_conda_recipe_init
+--help``.
+
+**Usage**::
+
+    planemo bioc_conda_recipe_init [OPTIONS]
+
+**Help**
+
+Make a bioconda recipe, given a R or bioconductor package name.
+
+package_name = motifbreakR
+
+bioconda_dir = '/Users/nturaga/Documents/workspace'.
+
+**Options**::
+
+
+      -u, --update / --no_update    Update an existing bioconda recipe
+      -b, --bioconda_dir_path TEXT  Give the path to folder containing bioconda
+                                    repository
+      -c, --clone / --no_clone      Clone bioconda repository from github or not?
+      -p, --package_name TEXT       Give the name of a Bioconductor package to
+                                    create a new bioconda recipe
+      --help                        Show this message and exit.
+

docs/commands/bioc_tool_init.rst

@@ -0,0 +1,54 @@
+
+``bioc_tool_init`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``bioc_tool_init``. This help message can be generated with ``planemo bioc_tool_init
+--help``.
+
+**Usage**::
+
+    planemo bioc_tool_init [OPTIONS]
+
+**Help**
+
+Generate a bioconductor tool outline from supplied arguments.
+**Options**::
+
+
+      -i, --id TEXT             Short identifier for new tool (no whitespace)
+      -f, --force               Overwrite existing tool if present.
+      -t, --tool PATH           Output path for new tool (default is <id>.xml)
+      -n, --name TEXT           Name for new R/Bioconductor tool (user facing).
+      -d, --description TEXT    Short description for new tool (user facing)
+      -c, --command TEXT        Command potentially including cheetah variables
+                                ()(e.g. 'seqtk seq -a $input > $output')
+      --rscript PATH            Name of an R script from which to create a Tool
+                                definition file. Requires use of --input and
+                                --output arguments. (e.g. --rscript 'file.R')
+      --rversion TEXT           R version this tool requries, if not given, the tool
+                                defaults to R 3.2.1, (eg: --rversion 'R 3.2.1').
+                                This option adds the R dependency in the tool
+                                requirements.
+      --input TEXT              An input description (e.g. input.fasta)
+      --output TEXT             An output location (e.g. output.bam), the Galaxy
+                                datatype is inferred from the extension.
+      --requirement TEXT        Name of the R/Bioconductor package. Requirements
+                                will be set using Bioconda. (e.g. --requirement
+                                'affy')
+      --help_text TEXT          Help text (reStructuredText)
+      --doi TEXT                Supply a DOI (http://www.doi.org/) easing citation
+                                of the tool for Galxy users (e.g. 10.1101/014043).
+      --cite_url TEXT           Supply a URL for citation.
+      --version TEXT            Tool XML version.
+      --help_from_command TEXT  Auto populate help from supplied command.
+      --test_case               For use with --example_commmand, generate a tool
+                                test case from the supplied example.
+      --macros                  Generate a macros.xml for reuse across many tools.
+      --named_output TEXT       Create a named output for use with command block for
+                                example specify --named_output=output1.bam and then
+                                use '-o $output1' in your command block.
+      --bioconda_path TEXT      Path to bioconda repository. If left empty, path
+                                will be made in home directory.
+      --help                    Show this message and exit.
+

docs/commands/brew.rst

@@ -12,7 +12,7 @@ This section is auto-generated from the help text for the planemo command
 
 **Help**
 
-Install tool requirements using brew. (**Experimental**)
+Install tool requirements using brew.
 
 An experimental approach to versioning brew recipes will be used.
 See full discussion on the homebrew-science issues page here -

docs/commands/brew_env.rst

@@ -12,8 +12,12 @@ This section is auto-generated from the help text for the planemo command
 
 **Help**
 
+List commands to inject brew dependencies.
+
 Display commands used to modify environment to inject tool's brew
-dependencies.::
+dependencies.
+
+::
 
     % . <(planemo brew_env bowtie2.xml)
     % which bowtie2
@@ -25,7 +29,9 @@ flag.
 
 Intead of injecting the enviornment into your current shell using the above
 idiom, the ``--shell`` flag can be sent to launch a new subshell when
-sourced.::
+sourced.
+
+::
 
     % . <(planemo brew_env --skip_install --shell bowtie2.xml)
     (bowtie2) % which bowtie2

docs/commands/brew_init.rst

@@ -12,8 +12,9 @@ This section is auto-generated from the help text for the planemo command
 
 **Help**
 
-Download linuxbrew install and run it with ruby. Linuxbrew is a fork
-of Homebrew (http://brew.sh/linuxbrew/).
+Download linuxbrew install & run it in ruby.
+
+Linuxbrew is a fork of Homebrew (http://brew.sh/linuxbrew/).
 
 For more information on installing linuxbrew and pre-requisites see
 https://github.com/Homebrew/linuxbrew#installation.

docs/commands/ci_find_repos.rst

@@ -0,0 +1,33 @@
+
+``ci_find_repos`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``ci_find_repos``. This help message can be generated with ``planemo ci_find_repos
+--help``.
+
+**Usage**::
+
+    planemo ci_find_repos [OPTIONS] PROJECT
+
+**Help**
+
+Find all shed repositories in one or more directories.
+
+Currently, a shed repository is considered a directory with a .shed.yml
+file.
+
+**Options**::
+
+
+      --exclude PATH                  Paths to exclude.
+      --exclude_from PATH             File of paths to exclude.
+      --changed_in_commit_range TEXT  Exclude paths unchanged in git commit range.
+      --chunk_count INTEGER           Split output into chunks of this many item and
+                                      print --chunk such group.
+      --chunk INTEGER                 When output is split into --chunk_count
+                                      groups, output the group 0-indexedby this
+                                      option.
+      --output TEXT                   File to output to, or - for standard output.
+      --help                          Show this message and exit.
+

docs/commands/ci_find_tools.rst

@@ -0,0 +1,33 @@
+
+``ci_find_tools`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``ci_find_tools``. This help message can be generated with ``planemo ci_find_tools
+--help``.
+
+**Usage**::
+
+    planemo ci_find_tools [OPTIONS] PROJECT
+
+**Help**
+
+Find all tools in one or more directories.
+
+Tools can be chunked up, filtered, etc... to build lists of tools to perform
+operations over for continuous integration operations.
+
+**Options**::
+
+
+      --exclude PATH                  Paths to exclude.
+      --exclude_from PATH             File of paths to exclude.
+      --changed_in_commit_range TEXT  Exclude paths unchanged in git commit range.
+      --chunk_count INTEGER           Split output into chunks of this many item and
+                                      print --chunk such group.
+      --chunk INTEGER                 When output is split into --chunk_count
+                                      groups, output the group 0-indexedby this
+                                      option.
+      --output TEXT                   File to output to, or - for standard output.
+      --help                          Show this message and exit.
+

docs/commands/clone.rst

@@ -0,0 +1,39 @@
+
+``clone`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``clone``. This help message can be generated with ``planemo clone
+--help``.
+
+**Usage**::
+
+    planemo clone [OPTIONS] TARGET PROJECT
+
+**Help**
+
+Short-cut to quickly clone, fork, and branch a relevant Github repo.
+
+For instance, the following will clone, fork, and branch the tools-iuc
+repository to allow a subsequent pull request to fix a problem with bwa.
+
+
+::
+
+    $ planemo clone --branch bwa-fix tools-iuc
+    $ cd tools-iuc
+    $ # Make changes.
+    $ git add -p # Add desired changes.
+    $ git commit -m "Fix bwa problem."
+    $ planemo pull_request -m "Fix bwa problem."
+
+These changes do require that a github username and password are
+specified in ~/.planemo.yml.
+
+**Options**::
+
+
+      --fork / --skip_fork
+      --branch TEXT         Create a named branch on result.
+      --help                Show this message and exit.
+

docs/commands/conda_env.rst

@@ -12,20 +12,30 @@ This section is auto-generated from the help text for the planemo command
 
 **Help**
 
-Source output to activate a conda environment for this tool.
+Activate a conda environment for tool.
+
+Source the output of this command to activate a conda environment for this
+tool.
+
+::
+
+    $ . <(planemo conda_env seqtk_seq.xml)
+    Deactivate environment with conda_env_deactivate
+    (seqtk_seq_v6) $ which seqtk
+    /home/planemo/miniconda2/envs/jobdepsDkzcjjfecc6d406196737781ff4456ec60975c137e04884e4f4b05dc68192f7cec4656/bin/seqtk
+    (seqtk_seq_v6) $ conda_env_deactivate
+    $
 
-    % . <(planemo conda_env bowtie2.xml)
-    % which bowtie2
-    TODO_PLACE_PATH_HERE
 
 **Options**::
 
 
-      --conda_prefix DIRECTORY      Conda prefix to use for conda dependency
-                                    commands.
-      --conda_exec PATH             Location of conda executable.
-      --conda_debug                 Enable more verbose conda logging.
-      --conda_ensure_channels TEXT  Ensure conda is configured with specified comma
-                                    separated list of channels.
-      --help                        Show this message and exit.
+      --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
+                                      commands.
+      --conda_exec PATH               Location of conda executable.
+      --conda_debug                   Enable more verbose conda logging.
+      --conda_channels, --conda_ensure_channels TEXT
+                                      Ensure conda is configured with specified
+                                      comma separated list of channels.
+      --help                          Show this message and exit.
 

docs/commands/conda_init.rst

@@ -21,14 +21,18 @@ By running this command, you are agreeing to the terms of the conda
 license a 3-clause BSD 3 license. Please review full license at
 http://docs.continuum.io/anaconda/eula.
 
+Planemo will print a warning and terminate with an exit code of 7
+if Conda is already installed.
+
 **Options**::
 
 
-      --conda_prefix DIRECTORY      Conda prefix to use for conda dependency
-                                    commands.
-      --conda_exec PATH             Location of conda executable.
-      --conda_debug                 Enable more verbose conda logging.
-      --conda_ensure_channels TEXT  Ensure conda is configured with specified comma
-                                    separated list of channels.
-      --help                        Show this message and exit.
+      --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
+                                      commands.
+      --conda_exec PATH               Location of conda executable.
+      --conda_debug                   Enable more verbose conda logging.
+      --conda_channels, --conda_ensure_channels TEXT
+                                      Ensure conda is configured with specified
+                                      comma separated list of channels.
+      --help                          Show this message and exit.
 

docs/commands/conda_install.rst

@@ -8,19 +8,30 @@ This section is auto-generated from the help text for the planemo command
 
 **Usage**::
 
-    planemo conda_install [OPTIONS] TOOL_PATH
+    planemo conda_install [OPTIONS] TARGET
 
 **Help**
 
 Install conda packages for tool requirements.
 **Options**::
 
 
-      --conda_prefix DIRECTORY      Conda prefix to use for conda dependency
-                                    commands.
-      --conda_exec PATH             Location of conda executable.
-      --conda_debug                 Enable more verbose conda logging.
-      --conda_ensure_channels TEXT  Ensure conda is configured with specified comma
-                                    separated list of channels.
-      --help                        Show this message and exit.
+      --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
+                                      commands.
+      --conda_exec PATH               Location of conda executable.
+      --conda_debug                   Enable more verbose conda logging.
+      --conda_channels, --conda_ensure_channels TEXT
+                                      Ensure conda is configured with specified
+                                      comma separated list of channels.
+      --global                        Install Conda dependencies globally instead of
+                                      in requirement specific environments packaged
+                                      for tools. If the Conda bin directory is on
+                                      your PATH, tools may still use binaries but
+                                      this is more designed for interactive testing
+                                      and debugging.
+      --conda_auto_init / --no_conda_auto_init
+                                      Conda dependency resolution for Galaxy will
+                                      auto install conda itself using miniconda if
+                                      not availabe on conda_prefix.
+      --help                          Show this message and exit.