[galaxy-commits] [galaxyproject/galaxy] 7e8bee: Deleting directories from SVN that should have bee...

GitHub noreply at github.com
Fri Sep 16 11:21:35 EDT 2016


  Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 7e8bee8830d5d82e222b350d4bc240d1206e5af3
      https://github.com/galaxyproject/galaxy/commit/7e8bee8830d5d82e222b350d4bc240d1206e5af3
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    A galaxy.xsd

  Log Message:
  -----------
  Deleting directories from SVN that should have been ignored.

git-svn-id: https://svn.msi.umn.edu/tint/trunk@427 29e1c259-b37a-0410-ae23-5fb2df606144


  Commit: 39fb238e666bb404b140b9ec37f1caeeb8a2637f
      https://github.com/galaxyproject/galaxy/commit/39fb238e666bb404b140b9ec37f1caeeb8a2637f
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Work on galaxy support, implemented repeat blocks in the UI.


  Commit: a718608e838f796bddb159b4e303194db52b3085
      https://github.com/galaxyproject/galaxy/commit/a718608e838f796bddb159b4e303194db52b3085
  Author: Jean-Frédéric <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    A README.md

  Log Message:
  -----------
  Add basic ReadMe


  Commit: 6e689fa77eef72020f62e00149bddfae825e299f
      https://github.com/galaxyproject/galaxy/commit/6e689fa77eef72020f62e00149bddfae825e299f
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Remove custom namespaces


  Commit: e1fc626fc1d6f2e49519784bea217ea3022d4073
      https://github.com/galaxyproject/galaxy/commit/e1fc626fc1d6f2e49519784bea217ea3022d4073
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Change tool element to <xs:all>

Element order is not enforced by Galaxy.


  Commit: 025a22b0e7bbb8f9fc89dac33c8e18fdfc49b36f
      https://github.com/galaxyproject/galaxy/commit/025a22b0e7bbb8f9fc89dac33c8e18fdfc49b36f
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add <requirements> tag set

This includes:
-<requirements>
-<requirement>
-Enumeration RequirementType


  Commit: 08f1faad44fde20cf0748d7c12785300d67942ec
      https://github.com/galaxyproject/galaxy/commit/08f1faad44fde20cf0748d7c12785300d67942ec
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Complete <repeat> tag set

Add attributes min and max to Repeat element


  Commit: 9a9ba49caab8c63cff05153948160acccd80f912
      https://github.com/galaxyproject/galaxy/commit/9a9ba49caab8c63cff05153948160acccd80f912
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add <options> tag to <param>

The <param> tag can contain <options> to dynamically create a list of options.


  Commit: 6b828d2b29b1612c82bcd7348625318628712aaf
      https://github.com/galaxyproject/galaxy/commit/6b828d2b29b1612c82bcd7348625318628712aaf
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add <label> tag to <param>


  Commit: 150939e16a242a992d69bb771a6bf87f1936be40
      https://github.com/galaxyproject/galaxy/commit/150939e16a242a992d69bb771a6bf87f1936be40
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add missing attributes to <param> tag

Add seven missing attributes to <param> tag
Add the necessary datatypes for display, hierarchy and checked.


  Commit: 62c32df6f1d7de93f04cd3a9b5fd7572f91f4363
      https://github.com/galaxyproject/galaxy/commit/62c32df6f1d7de93f04cd3a9b5fd7572f91f4363
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add missing attributes and element to <data> tag

Add three missing attributes to <data> tag
Add <filter> element to sequence


  Commit: 73edfd6cf03c4366d4fd1036aa6fe3760958cd2a
      https://github.com/galaxyproject/galaxy/commit/73edfd6cf03c4366d4fd1036aa6fe3760958cd2a
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Fix indentation


  Commit: 91a166b7f5f42ee60495da20443b73d4bda1a502
      https://github.com/galaxyproject/galaxy/commit/91a166b7f5f42ee60495da20443b73d4bda1a502
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add <parallelism> tag

Add the <parallelism> tag (which serves for splitting job)
and the datatype for the 'method' attribute.


  Commit: f9c5cf28ef2f60867a81dd8b6da3454e46d2936a
      https://github.com/galaxyproject/galaxy/commit/f9c5cf28ef2f60867a81dd8b6da3454e46d2936a
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add <stdio> tag set to <tool>

Add <stdio> tag set, to handle tool messages on standard output
and standard error.

- Add <stdio> tag
- Add <regex> and <exit_code> sub elements
- Add datatypes for 'range', 'level' and 'source' attributes


  Commit: 6e1d7e40a333d717a7c877c18eb94048dd99a7f0
      https://github.com/galaxyproject/galaxy/commit/6e1d7e40a333d717a7c877c18eb94048dd99a7f0
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Change type for requirement version

Version information can be too complex for xs:decimal
(eg "0.12.7"). Change for xs:string.


  Commit: 642e88857caa09d968f4e5c740dc44475a64e288
      https://github.com/galaxyproject/galaxy/commit/642e88857caa09d968f4e5c740dc44475a64e288
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add column, filter and validator tags


  Commit: 1787f1e89b4a311d9bae2c60effc851347da50e2
      https://github.com/galaxyproject/galaxy/commit/1787f1e89b4a311d9bae2c60effc851347da50e2
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add ftype attribute to param tag in tests


  Commit: 6181d24704fd23b3370a961ba3fb573d0100f099
      https://github.com/galaxyproject/galaxy/commit/6181d24704fd23b3370a961ba3fb573d0100f099
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add <code> tag set


  Commit: 0da4d3c85361954a82fb8a0aa4c0f6bd742b9033
      https://github.com/galaxyproject/galaxy/commit/0da4d3c85361954a82fb8a0aa4c0f6bd742b9033
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Remove required use from <requirement> version


  Commit: 8164cfd3ba691dbb11fc5f623610b726ad5f2b85
      https://github.com/galaxyproject/galaxy/commit/8164cfd3ba691dbb11fc5f623610b726ad5f2b85
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Edit <options> tag set


  Commit: bb285e4caee908cf4be30f0bf19ae21ffba20ebe
      https://github.com/galaxyproject/galaxy/commit/bb285e4caee908cf4be30f0bf19ae21ffba20ebe
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add <validator> to <param>


  Commit: 02aa90c4a477bb595540914df08ef9402275d84d
      https://github.com/galaxyproject/galaxy/commit/02aa90c4a477bb595540914df08ef9402275d84d
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add 'split' attribute to <validator>


  Commit: e200148feef9ff553820272d7893b387e6e4723d
      https://github.com/galaxyproject/galaxy/commit/e200148feef9ff553820272d7893b387e6e4723d
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add <actions> tag set


  Commit: 1c9513d6cb64315e742eab7befec7536dee766c8
      https://github.com/galaxyproject/galaxy/commit/1c9513d6cb64315e742eab7befec7536dee766c8
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Extend CheckedType to accept unspecified values

According to the documentation, CheckedType can either
be 'yes', 'true' or 'on' ; but many tools use '[Ff]alse'
which seems to be accepted/ignored by Galaxy.


  Commit: b35b9fd52c78a891555660d7512e617b03d36cc0
      https://github.com/galaxyproject/galaxy/commit/b35b9fd52c78a891555660d7512e617b03d36cc0
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add PermissiveBoolean datatype

<xs:boolean> can either be 'true', 'false', '1' or 'O' ; but many
Galaxy tools use 'True' and 'False' (capitalized), which appears
to be ignored/accepted by Galaxy.
This PermissiveBoolean type is meant to be used in place of xs:boolean
when needed.


  Commit: dd0ba4293dc03db422a7b33e974c3b7554c287e9
      https://github.com/galaxyproject/galaxy/commit/dd0ba4293dc03db422a7b33e974c3b7554c287e9
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add attributes 'ftype' and 'sort' to test <output>

These are undocumented attributes.


  Commit: 4578e0a0f957ef7f851257b7bb605764712c5a44
      https://github.com/galaxyproject/galaxy/commit/4578e0a0f957ef7f851257b7bb605764712c5a44
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) attributes to <filter>

Add attributes 'compare', 'keep' and 'value' to <filter> tag
(though these attributes are not documented).
Add CompareType for possible 'compare' values.


  Commit: 4bdfd455c58d00c5a28fdf1e6fc80d70648cb57a
      https://github.com/galaxyproject/galaxy/commit/4bdfd455c58d00c5a28fdf1e6fc80d70648cb57a
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Edit filter tag for output tag


  Commit: 566e279172c98e417c7fca9cf04bda2e3abd2da5
      https://github.com/galaxyproject/galaxy/commit/566e279172c98e417c7fca9cf04bda2e3abd2da5
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Rewrite <actions> handling


  Commit: 1cda2e4439f28229d000f30120ecf69709606b6f
      https://github.com/galaxyproject/galaxy/commit/1cda2e4439f28229d000f30120ecf69709606b6f
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) 'dbkey' attribute to TestParam


  Commit: 081c39e55161e1d1babebed1d159f2415a8e0adb
      https://github.com/galaxyproject/galaxy/commit/081c39e55161e1d1babebed1d159f2415a8e0adb
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add 'from_file' value to ActionsOptionType


  Commit: b466de7e0a5e019d1a4264f2982f8c2012715241
      https://github.com/galaxyproject/galaxy/commit/b466de7e0a5e019d1a4264f2982f8c2012715241
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Use PermissiveBoolean for ParamOption 'selected'


  Commit: 92b1076261ee0403ff8fb6f8e2601ba5149e9807
      https://github.com/galaxyproject/galaxy/commit/92b1076261ee0403ff8fb6f8e2601ba5149e9807
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add attributes tool_type and URL_method to <tool>

And corresponding enumeration Datatypes.


  Commit: e8f236a52e5c4081ef9a228e15ffefb50185db7f
      https://github.com/galaxyproject/galaxy/commit/e8f236a52e5c4081ef9a228e15ffefb50185db7f
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  use PermissiveBoolean on two attributes of <param>


  Commit: 7d7b5a8d3dfc604335626f0abf806377dc2b630c
      https://github.com/galaxyproject/galaxy/commit/7d7b5a8d3dfc604335626f0abf806377dc2b630c
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) value 'no' to CheckedType


  Commit: e19f1fb99a982cedebc74a3b42f0c376e19d46bc
      https://github.com/galaxyproject/galaxy/commit/e19f1fb99a982cedebc74a3b42f0c376e19d46bc
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) <uihints> to <tool>

See /lib/galaxy/tools/__init__.py:1069 for usage


  Commit: 836aff4b3f70d6073bbd5f4d78d4b6688aed7baa
      https://github.com/galaxyproject/galaxy/commit/836aff4b3f70d6073bbd5f4d78d4b6688aed7baa
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) attributes to <inputs>

Add attributes 'action', 'check_values', 'method' and 'target'
to <inputs>.
Add relevant Target datatype.


  Commit: c4769e701302625031db4a7730e572b32c019ead
      https://github.com/galaxyproject/galaxy/commit/c4769e701302625031db4a7730e572b32c019ead
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add <sanitizer> tag


  Commit: 5419b1a4bce60a4459b59711acbf9c2652d5722d
      https://github.com/galaxyproject/galaxy/commit/5419b1a4bce60a4459b59711acbf9c2652d5722d
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) attribute metadata_name to <param>


  Commit: 79cf1c57d8b6a1add066bf61ec18936bf1a8f6ee
      https://github.com/galaxyproject/galaxy/commit/79cf1c57d8b6a1add066bf61ec18936bf1a8f6ee
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) attributes to <options>

Add 'options_filter_attribute' attribute
(see lib/galaxy/tools/parameters/basic.py)
Add 'transform_lines' attribute
(see lib/galaxy/tools/parameters/dynamic_options.py)
transform_lines and


  Commit: 11b013f402b90c742789df87b6810e156a173171
      https://github.com/galaxyproject/galaxy/commit/11b013f402b90c742789df87b6810e156a173171
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) 'ref_attribute' to <filter>

Add attribute 'ref_attribute' to <filter>
(see lib/galaxy/tools/parameters/dynamic_options.py:153)


  Commit: 65903327fa21536d44822ef94a9e75b2d29cf11d
      https://github.com/galaxyproject/galaxy/commit/65903327fa21536d44822ef94a9e75b2d29cf11d
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) 'startswith' to <options>

Add attribute 'startswith' to <options> tag
(see lib/galaxy/tools/parameters/dynamic_options.py:416)


  Commit: d12766e260ea8d1e6ebe61806cb7e2b3eb55b886
      https://github.com/galaxyproject/galaxy/commit/d12766e260ea8d1e6ebe61806cb7e2b3eb55b886
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add (undocumented) attribute 'display' to <inputs>

See lib/galaxy/tools/__init__.py:1531


  Commit: 091b3b85687eeb8ef5becdf30ff81211b12f6f45
      https://github.com/galaxyproject/galaxy/commit/091b3b85687eeb8ef5becdf30ff81211b12f6f45
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Fix value baseurl in <param> 'type' attribute


  Commit: 395780d3d143982204c1f9ccf188df1deff51d55
      https://github.com/galaxyproject/galaxy/commit/395780d3d143982204c1f9ccf188df1deff51d55
  Author: JeanFred <jean-frederic.berthelot at lifl.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Fix type of min and max in <validator>


  Commit: 2fdf2267b841d2701db424f9d2f458d8fbc2309b
      https://github.com/galaxyproject/galaxy/commit/2fdf2267b841d2701db424f9d2f458d8fbc2309b
  Author: Pierre Lindenbaum <plindenbaum at yahoo.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    A .gitignore
    A Makefile
    M README.md
    A citation.xsd
    A citations.xsd
    A galaxy.jxb
    M galaxy.xsd
    A test.urls

  Log Message:
  -----------
  added doc and JXB bindings


  Commit: 2cecbe1922a9b5d75f34d42bedcd025a83fbae09
      https://github.com/galaxyproject/galaxy/commit/2cecbe1922a9b5d75f34d42bedcd025a83fbae09
  Author: Pierre Lindenbaum <plindenbaum at yahoo.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M README.md

  Log Message:
  -----------
  updated README


  Commit: f692d3a5ae244ce638be596723f369dade3ed501
      https://github.com/galaxyproject/galaxy/commit/f692d3a5ae244ce638be596723f369dade3ed501
  Author: Jean-Fred <JeanFred at github>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    A .travis.yml

  Log Message:
  -----------
  Add Continuous integration with Travis for XSD linting

At the very least these XSD files should be XML valid.


  Commit: cdbe79b4b657609724081c991466b0be13460d36
      https://github.com/galaxyproject/galaxy/commit/cdbe79b4b657609724081c991466b0be13460d36
  Author: Jean-Fred <JeanFred at github>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M .travis.yml

  Log Message:
  -----------
  Fix dependency installation for Travis

Build was failing with
$ apt-get install libxml2-utils
E: Could not open lock file /var/lib/dpkg/lock - open (13: Permission denied)
E: Unable to lock the administration directory (/var/lib/dpkg/), are you root?

APT dependencies must be installed as sudoer.


  Commit: 00a560ce1dbb093989b36f628abf08bf5ad3ee91
      https://github.com/galaxyproject/galaxy/commit/00a560ce1dbb093989b36f628abf08bf5ad3ee91
  Author: Jean-Fred <JeanFred at github>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M README.md

  Log Message:
  -----------
  Add Travis badge to ReadMe


  Commit: 3315e9a8c424281df01e7521a9c9715447356059
      https://github.com/galaxyproject/galaxy/commit/3315e9a8c424281df01e7521a9c9715447356059
  Author: Jean-Fred <JeanFred at github>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    A test.sh

  Log Message:
  -----------
  Add Shell test script

Following the idea of @lindenb in the Makefile.

This tests all the given URLs in test.urls and
outputs a compliant TAP.


  Commit: bcc20e289fc9c4df1615530b264a6cada2e39974
      https://github.com/galaxyproject/galaxy/commit/bcc20e289fc9c4df1615530b264a6cada2e39974
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M README.md

  Log Message:
  -----------
  Add me (@jmchilton) to authors list.

My name is on the earliest commits (thanks for preserving that).


  Commit: 1b7f2a54f6c2b12d9340fe4c8c3e8de0f0f68afb
      https://github.com/galaxyproject/galaxy/commit/1b7f2a54f6c2b12d9340fe4c8c3e8de0f0f68afb
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M citation.xsd
    M test.urls

  Log Message:
  -----------
  Fix CitationType attribute.

Add Galaxy's test tool for citations to test.urls.


  Commit: 057c36997bd5c4c75a85acd5a9346f8c28eee015
      https://github.com/galaxyproject/galaxy/commit/057c36997bd5c4c75a85acd5a9346f8c28eee015
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd
    M test.urls

  Log Message:
  -----------
  Update XSD for container tags.

Add Galaxy test tool for Docker container tags to test.urls.


  Commit: bdf36556fbf4c4db4c343e51d6d78c1ac2030464
      https://github.com/galaxyproject/galaxy/commit/bdf36556fbf4c4db4c343e51d6d78c1ac2030464
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Drop embeddedValue for test stuff.

These were an extension to the Galaxy XML syntax for TINT - which is no longer actively maintained.


  Commit: f0799b5fbb9dfe54241b702c450f258c946bf326
      https://github.com/galaxyproject/galaxy/commit/f0799b5fbb9dfe54241b702c450f258c946bf326
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd
    M test.urls

  Log Message:
  -----------
  Start work on implementing assert_contents tag in tests.

Just enough to get Galaxy's simple_contructrs.xml to validate - add this to test.urls. More work should be done on these - but it should be automated derived from Galaxy somehow.


  Commit: b479b7334fc6649606c5144da7c9225c82857e6b
      https://github.com/galaxyproject/galaxy/commit/b479b7334fc6649606c5144da7c9225c82857e6b
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd
    M test.urls

  Log Message:
  -----------
  Update XSD for very basic data collection usage.

 - Allow 'data_collection' parameters and allow them to specify a 'collection_type'.
 - Allow test parameters to be flat collections.
 - Add test/functional/tools/collection_paired_test.xml to test.urls to check all of this.

Lots more TODO for recent tool collection support - output collections definitions, output collection tests, dynamic discovery tags, specifying nested collections for test inputs.


  Commit: 49f7d51f57eb2f72e01e37fdaf6c44ffe11898de
      https://github.com/galaxyproject/galaxy/commit/49f7d51f57eb2f72e01e37fdaf6c44ffe11898de
  Author: Jean-Fred <JeanFred at github>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    A LICENSE
    M README.md

  Log Message:
  -----------
  Add MIT license

Per agreement of all authors.

Closes #2.


  Commit: 8947f29ef2596e750d2783206df547efc7ef40fd
      https://github.com/galaxyproject/galaxy/commit/8947f29ef2596e750d2783206df547efc7ef40fd
  Author: Jean-Fred <JeanFred at github>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M README.md

  Log Message:
  -----------
  Expand history in ReadMe


  Commit: 5d40c7b3e2b66d91a52ae12cf48cda30d245d180
      https://github.com/galaxyproject/galaxy/commit/5d40c7b3e2b66d91a52ae12cf48cda30d245d180
  Author: Jean-Fred <JeanFred at github>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M LICENSE

  Log Message:
  -----------
  Fix authors in License file

Follow up on #2.


  Commit: a4e5568af7f206c61ebf7afd9165bd1e34181d0b
      https://github.com/galaxyproject/galaxy/commit/a4e5568af7f206c61ebf7afd9165bd1e34181d0b
  Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  first try


  Commit: 8f8cc890bcfaceaf4870daa2d4e22e10018119c2
      https://github.com/galaxyproject/galaxy/commit/8f8cc890bcfaceaf4870daa2d4e22e10018119c2
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Improvements to XSD:

- Implement section.
- Implement and document request_parameter_translation, request_parameter and its children (value_translation and append_param).
- Implement detect_errors on the command block and document defaults.


  Commit: 63c019b13b44fedc9159909eb7995294d3653244
      https://github.com/galaxyproject/galaxy/commit/63c019b13b44fedc9159909eb7995294d3653244
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More progress...

- Fix to previous commit.
- Remove downstream config file type that was abandoned work and not in galaxy-core.
- More documentation for configfile stuff.
- Improvements to representation for output and santizer.


  Commit: 1125f1b8ea8b993ac5493f663b76c4ba54350ee4
      https://github.com/galaxyproject/galaxy/commit/1125f1b8ea8b993ac5493f663b76c4ba54350ee4
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Simplify schema and improve docs related to sanitization.


  Commit: 21cd752e252d17fdba2401cbe78bc3ef62ffd327
      https://github.com/galaxyproject/galaxy/commit/21cd752e252d17fdba2401cbe78bc3ef62ffd327
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Improve docs on filter and change_format of outputs.


  Commit: 804c072d5af2e5704d57a503a84ad6733f03c1c0
      https://github.com/galaxyproject/galaxy/commit/804c072d5af2e5704d57a503a84ad6733f03c1c0
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  And more progress...

- Docs for help.
- Docs for tests.
- Docs for code files.
- Implementing more of the assert_xxx test flags.
- Improved coverage of test assertion element descriptions.


  Commit: 23449750d46e4df208fc46d1c2a4d3840cd080f4
      https://github.com/galaxyproject/galaxy/commit/23449750d46e4df208fc46d1c2a4d3840cd080f4
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More progress...

- Refine test outputs and include syntax for testing extra files and md5sums.


  Commit: 3d3c3fee4f576408c223c723b57b003ae6ccf4c1
      https://github.com/galaxyproject/galaxy/commit/3d3c3fee4f576408c223c723b57b003ae6ccf4c1
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More progress.

- Add strict to command.
- Add conditional and repeat to test params.
- Add count to output collections.
- Implement more collection output attributes (type_source, etc...).
- Reduce need for type on collection defs (since type_source can be defined).


  Commit: 80d086b861f1401568b967d96e2e37461ca677a2
      https://github.com/galaxyproject/galaxy/commit/80d086b861f1401568b967d96e2e37461ca677a2
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More progress...

- Allow section in test parameters.
- Implement basic metadata testing.


  Commit: 19b273cdf55df6b2593715d7daaf4690d8d6935b
      https://github.com/galaxyproject/galaxy/commit/19b273cdf55df6b2593715d7daaf4690d8d6935b
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More progress...

- Allow nested elements in test output collections (hackily)
- Implement ``compare`` and ``delta`` for test output comparison.
- Implement the new ``checksum`` output test.


  Commit: 7f5cc04c114bd5e696e7e54697e5a7bf58277fa7
      https://github.com/galaxyproject/galaxy/commit/7f5cc04c114bd5e696e7e54697e5a7bf58277fa7
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More progress...

- Add tool action.
- Stub workflow_compatible and profile_version attributes on tool.
- Add many more attributes to parallelism tag.
- Add maxseconds and expect_num_outputs to tool test tag.
- Small fix to <repeat> block in test cases.
- Implement assigning metadata in test params.
- Allow more versitle ordering of test blocks (too permissive now).
- Implement testing of output metadata and discovered datasets.
- Add nginx_upload attribute used by upload.xml and various conditional attributes for pulling in values from Galaxy internals.
- Implement the stub of a ``upload_dataset`` param and say not to use it.
- Add color and library data parameter types.
- More attributes to filters and validators.
- Implement auto_format on outputs.
- Implement filters and explicit data outputs on output collections.
- Implement inputs as json element.
- Add empty dataset validator.


  Commit: 49ff357854ff1a8dab9d792c0d97881f33c5a603
      https://github.com/galaxyproject/galaxy/commit/49ff357854ff1a8dab9d792c0d97881f33c5a603
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Stub out environment variables and add a new tool type.


  Commit: c6ae6ee8cb3c240923e4738f0e8f0a4a1134cbd5
      https://github.com/galaxyproject/galaxy/commit/c6ae6ee8cb3c240923e4738f0e8f0a4a1134cbd5
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    R citation.xsd
    R citations.xsd
    M galaxy.xsd

  Log Message:
  -----------
  Embed citations right in galaxy.xsd.

Not that I mind splitting it up - but it will make a couple things easier downstream and those few tags weren't enough to warrent breaking things up like that.


  Commit: dcfdd3ceaa62ccee0a8d22c6d299eab2742df47f
      https://github.com/galaxyproject/galaxy/commit/dcfdd3ceaa62ccee0a8d22c6d299eab2742df47f
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Many more fixes derived from testing tools-iuc.


  Commit: 8c2a4e12758827b0855181de962ef0f0a61515a7
      https://github.com/galaxyproject/galaxy/commit/8c2a4e12758827b0855181de962ef0f0a61515a7
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  And more progress - now covers all Galaxy test tools and all IUC.

- Add <options> block.
- Add <trackster_conf> block.
- Add a newerish validator and allow filter/validator columns to be column names.
- More permissives boolean values to match Galaxy in various places.
- Other mostly obsecure features.


  Commit: ff6cca8635e6ce1c906dd316dcc0d6ab0bed7fb3
      https://github.com/galaxyproject/galaxy/commit/ff6cca8635e6ce1c906dd316dcc0d6ab0bed7fb3
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Doc updates


  Commit: 491efe8c4951eedecc1635dbc972fb49ec883230
      https://github.com/galaxyproject/galaxy/commit/491efe8c4951eedecc1635dbc972fb49ec883230
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Doc improvements.


  Commit: 94ad78da97b98eee05a5ff0f890eec0e518845b7
      https://github.com/galaxyproject/galaxy/commit/94ad78da97b98eee05a5ff0f890eec0e518845b7
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Much richer documentation for a few tags including ``command``.


  Commit: e9f08b411a0bf4ef8620bc66fb7c10d61112fb49
      https://github.com/galaxyproject/galaxy/commit/e9f08b411a0bf4ef8620bc66fb7c10d61112fb49
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More work on documentation - revise last commit and add repeats and sections.


  Commit: 2e31bc932dd9bd96d403cd8e6ef20715785c3eef
      https://github.com/galaxyproject/galaxy/commit/2e31bc932dd9bd96d403cd8e6ef20715785c3eef
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Work on docs.


  Commit: 8f2f62a75a7aa256904821888c09682ebde99c83
      https://github.com/galaxyproject/galaxy/commit/8f2f62a75a7aa256904821888c09682ebde99c83
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More docs...

- Added docs for param's option.
- Started work on validators and options, but are WIP though.


  Commit: 4bcfe568b713e9369d0d1e5090e140d7ebfee17c
      https://github.com/galaxyproject/galaxy/commit/4bcfe568b713e9369d0d1e5090e140d7ebfee17c
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More docs for validators.


  Commit: 2980835dc7ec8b2ba2e1cde39142e0697c4fc9f8
      https://github.com/galaxyproject/galaxy/commit/2980835dc7ec8b2ba2e1cde39142e0697c4fc9f8
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  A lot more documentation around parameter options.

Also fixed a bit of a problem - turns out <filter> in action conditionals is very different than filter in options so I've split these types out.


  Commit: cd5328dce2aff381df95fa7b523dc40bc525f704
      https://github.com/galaxyproject/galaxy/commit/cd5328dce2aff381df95fa7b523dc40bc525f704
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More documentation...

Cleaned up the stdio tags and help section, flushed out citations and parameter options. Small touchups other places also.


  Commit: 24f46245e09ef044cca6804c48c994e49b70b69a
      https://github.com/galaxyproject/galaxy/commit/24f46245e09ef044cca6804c48c994e49b70b69a
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Mention code files as a way to generate dynamic options.

Transplant example from Galaxy wiki of doing this.


  Commit: 6481a00f88bff4bb7a7adbf2aaaee639e4649147
      https://github.com/galaxyproject/galaxy/commit/6481a00f88bff4bb7a7adbf2aaaee639e4649147
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Flush out docs for requirements and child tags.


  Commit: 3af76de52ff56fca6b65d993ce91fb39c30af2d2
      https://github.com/galaxyproject/galaxy/commit/3af76de52ff56fca6b65d993ce91fb39c30af2d2
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Flush out docs for sanitizers, configfiles, etc...


  Commit: b059c8b592b0f45dd669f8e9cbca714ed292ccac
      https://github.com/galaxyproject/galaxy/commit/b059c8b592b0f45dd669f8e9cbca714ed292ccac
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Working my way through basic parameter documentation.


  Commit: 366def7026a68e2bde75a140e3e4f1496966b1f2
      https://github.com/galaxyproject/galaxy/commit/366def7026a68e2bde75a140e3e4f1496966b1f2
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More work on parameters and environment variables.


  Commit: 4ba421e2f67de03dfa51ad8493f9a27beb159f27
      https://github.com/galaxyproject/galaxy/commit/4ba421e2f67de03dfa51ad8493f9a27beb159f27
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Finishing first pass at filling out wiki docs for ``param``.

And other small fixes.


  Commit: 5ad6e790e2f1a752beb748581469aa2e9f73477f
      https://github.com/galaxyproject/galaxy/commit/5ad6e790e2f1a752beb748581469aa2e9f73477f
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Starting to polish and flush out data outputs documentation.


  Commit: e2d55ccf1685ec767d2c09715b189c7a1ff411cb
      https://github.com/galaxyproject/galaxy/commit/e2d55ccf1685ec767d2c09715b189c7a1ff411cb
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  More docs - conditional output actions and some more on discover datasets.


  Commit: 89c8934727c7a8b8cc4ca7db10e7882d22542a87
      https://github.com/galaxyproject/galaxy/commit/89c8934727c7a8b8cc4ca7db10e7882d22542a87
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  A bunch of work on cleaning up and flushing out documentation for test tags.


  Commit: c607727d83c079a2859ed9026d26edbb52f4bcf9
      https://github.com/galaxyproject/galaxy/commit/c607727d83c079a2859ed9026d26edbb52f4bcf9
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Document the test ``output_collection`` tag.


  Commit: fc440a87c4883a9244d5e45783e2f27b639319cb
      https://github.com/galaxyproject/galaxy/commit/fc440a87c4883a9244d5e45783e2f27b639319cb
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Fix missing annotation.


  Commit: 60def6204d1ba2299442a76856f19ab53ffe1e92
      https://github.com/galaxyproject/galaxy/commit/60def6204d1ba2299442a76856f19ab53ffe1e92
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Fixes of structure broken with docs.


  Commit: b74c1a5b0baa6da94ca45f11a1e8e2057fcf2790
      https://github.com/galaxyproject/galaxy/commit/b74c1a5b0baa6da94ca45f11a1e8e2057fcf2790
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Use the new action conditional filter.


  Commit: 195fd46604a64ad8928ead83d6cd6f7f51a2639c
      https://github.com/galaxyproject/galaxy/commit/195fd46604a64ad8928ead83d6cd6f7f51a2639c
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Add a fictious XML schema with Galaxy stuff.

New attributes:

 - deprecated
 - best_practices (provides links of the form http://planemo.readthedocs.io/en/latest/standards/docs/best_practices/tool_xml.html#XXX)


  Commit: 4dd8da09b8bd1917094622039adfe01cffa2fd40
      https://github.com/galaxyproject/galaxy/commit/4dd8da09b8bd1917094622039adfe01cffa2fd40
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Remove embedded best practice stuff - the help will have links now.


  Commit: c4f03079d7fefb2e37790b4d07fe7d0a67990d8d
      https://github.com/galaxyproject/galaxy/commit/c4f03079d7fefb2e37790b4d07fe7d0a67990d8d
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Fill out some docs for test sections...


  Commit: 0c6be2095710fbb79bd9b9fdd231e960bb9f2ce8
      https://github.com/galaxyproject/galaxy/commit/0c6be2095710fbb79bd9b9fdd231e960bb9f2ce8
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M test.sh

  Log Message:
  -----------
  Revise automated testing, check against test tools and IUC tools.


  Commit: b9d25b848c333226e503d4f301187a43dbebc584
      https://github.com/galaxyproject/galaxy/commit/b9d25b848c333226e503d4f301187a43dbebc584
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Document testing discovered datasets and metadata.


  Commit: 8b7ae4bc7b446b0b00758f6cf0c98e7eaece96ce
      https://github.com/galaxyproject/galaxy/commit/8b7ae4bc7b446b0b00758f6cf0c98e7eaece96ce
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Fix a syntax error.


  Commit: 236bdf5a40d0d720a72b7c71b03e2cb79fc576d4
      https://github.com/galaxyproject/galaxy/commit/236bdf5a40d0d720a72b7c71b03e2cb79fc576d4
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M galaxy.xsd

  Log Message:
  -----------
  Update the link for multiple outputs.


  Commit: 3d7ae4e38fea3d7f84368ccb57f107f0c13f9749
      https://github.com/galaxyproject/galaxy/commit/3d7ae4e38fea3d7f84368ccb57f107f0c13f9749
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    R .gitignore
    R .travis.yml
    R LICENSE
    R Makefile
    R README.md
    R galaxy.jxb
    R galaxy.xsd
    A lib/galaxy/tools/xsd/LICENSE
    A lib/galaxy/tools/xsd/Makefile
    A lib/galaxy/tools/xsd/README.md
    A lib/galaxy/tools/xsd/galaxy.jxb
    A lib/galaxy/tools/xsd/galaxy.xsd
    A lib/galaxy/tools/xsd/test.sh
    A lib/galaxy/tools/xsd/test.urls
    R test.sh
    R test.urls

  Log Message:
  -----------
  Relocate Galaxy XSD files into Galaxy directory structure.


  Commit: 491c9fd519be37b6c6f57cd4082d981c9f411ba5
      https://github.com/galaxyproject/galaxy/commit/491c9fd519be37b6c6f57cd4082d981c9f411ba5
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    R lib/galaxy/tools/xsd/Makefile
    R lib/galaxy/tools/xsd/test.urls

  Log Message:
  -----------
  Cleanup XSD for move to Galaxy core.


  Commit: c4d8dddc5cbfe416e5931e409db9e63804688f1e
      https://github.com/galaxyproject/galaxy/commit/c4d8dddc5cbfe416e5931e409db9e63804688f1e
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    A lib/galaxy/tools/xsd/LICENSE
    A lib/galaxy/tools/xsd/README.md
    A lib/galaxy/tools/xsd/galaxy.jxb
    A lib/galaxy/tools/xsd/galaxy.xsd
    A lib/galaxy/tools/xsd/test.sh

  Log Message:
  -----------
  Merge branch 'master' of Galaxy-XSD into 'dev'


  Commit: babaf7a2c675648e2851f81d985a72321b4eeb44
      https://github.com/galaxyproject/galaxy/commit/babaf7a2c675648e2851f81d985a72321b4eeb44
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/xsd/galaxy.xsd
    R lib/galaxy/tools/xsd/test.sh

  Log Message:
  -----------
  Address reviewer comments on XSD.

- Merge in @bgruening's numerous awesome fixes.
- Remove test script with issues that make if not a fit for this repo in that form (noted by @nsoranzo).
- Incorporate other changes to the XSD suggested by @nsoranzo.


  Commit: 70251b5b6a8363a627fccf90f642c3a02cc57cd5
      https://github.com/galaxyproject/galaxy/commit/70251b5b6a8363a627fccf90f642c3a02cc57cd5
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/xsd/LICENSE

  Log Message:
  -----------
  Update the LICENSE for the XSD file.


  Commit: 9d24d55cb5e515b8e8f9654e070ae17aae864367
      https://github.com/galaxyproject/galaxy/commit/9d24d55cb5e515b8e8f9654e070ae17aae864367
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M CONTRIBUTORS.md

  Log Message:
  -----------
  Add XSD contributors to CONTRIBUTORS.md.


  Commit: f12723dc8311b35c9cf7271dc3bc46f640bde00b
      https://github.com/galaxyproject/galaxy/commit/f12723dc8311b35c9cf7271dc3bc46f640bde00b
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-09-16 (Fri, 16 Sep 2016)

  Changed paths:
    M CONTRIBUTORS.md
    A lib/galaxy/tools/xsd/LICENSE
    A lib/galaxy/tools/xsd/README.md
    A lib/galaxy/tools/xsd/galaxy.jxb
    A lib/galaxy/tools/xsd/galaxy.xsd

  Log Message:
  -----------
  Merge pull request #2923 from jmchilton/merge_xsd_into_core

Merge Galaxy-XSD into project


Compare: https://github.com/galaxyproject/galaxy/compare/31b4eb155fa8...f12723dc8311


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