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03eb852c2dbfc6591c46b72e056c51380b074819
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173 Commits
Author SHA1 Message Date
Nicola Soranzo 9cbabef17e Merge branch 'release_17.05' into dev 
Conflicts:
	static/maps/mvc/library/library-foldertoolbar-view.js.map
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/mvc/library/library-foldertoolbar-view.js
 2017-08-14 12:07:17 +01:00
Nicola Soranzo 4faf496c98 Merge branch 'release_17.01' into release_17.05 
Conflicts:
	tox.ini
 2017-08-14 11:54:55 +01:00
Björn Grüning c6e45e7b07 Merge pull request #4410 from jmchilton/excel97 
Add Excel97 Datatype
 2017-08-11 21:46:06 +02:00
Nicola Soranzo ba3249acf0 Add missing chemical formats to datatypes_conf.xml.sample 2017-08-10 20:36:50 +01:00
John Chilton bcdf2c84f6 Merge pull request #4254 from ffinfo/vcf_gz_datatype 
Vcf gz datatype
 2017-08-10 12:14:05 -04:00
John Chilton cf34d8b759 Merge pull request #4392 from bgruening/deeptools_datatypes 
Add deepTools datatypes to Galaxy
 2017-08-08 22:20:51 -04:00
Björn Grüning f8648b6586 Add deeptools datatypes to Galaxy 2017-08-08 19:24:40 +02:00
Björn Grüning e2f69a9c5b add imzml to the datatypes conf file 2017-08-02 21:40:39 +02:00
mvdbeek 63865e1193 Add VcfGz datatype 
This adds support for uploading VcfGz files in the upload box. When a
user does this, the file will not be uncompressed. Also adds
uncompressed preview.

TODO:
  - Move Vcf class to BaseVcf
  - Vcf and VcfGz should both inherit from BaseVcf
  - Add a metadata element for VcfGz indexes (vzf.gz.tbi)
  - Create index (in set_meta method of VcfGz class)
  - Write test tools

This is a kcikstart to @ffinfo GCC hack project.
 2017-07-07 18:29:05 +03:00
John Chilton 83b1988931 Refine new Excel XLS datatype. 
- Call it excel.xls so we maintain backward compatiblity with older xls datatype.
- Add an example file with a sniff test.
- Correct variable name for Python styling.
- Quote paths when using file command-line trick to sniff for the new type.
- Switch file command-line flag to one that produces the Mimetype on both Linux and Mac OS X.
 2017-07-05 14:51:25 -04:00
Greg Von Kuster 66dabf65ab Add ptkscmp datatype for PlantTribes significant components in the Ks distribution 2017-06-28 10:59:11 -04:00
Devon Ryan 0a942d79a3 Checking the quality lines will make fastqsanger checks rather more relevant. 2017-06-26 16:36:17 +02:00
Frederic Sapet 9cd9c81279 deals with .xls older file extension 2017-06-16 16:48:14 +02:00
Greg Von Kuster 507dc9d7fc Fix the Smat sniffer 2017-06-05 10:00:49 -04:00
Greg Von Kuster 72eb4858db Move PlantTribes datatypes to a separate file, will replace PR 3999 2017-06-01 08:32:04 -04:00
Jorrit Boekel c10a23b924 More recognizable naming for datatype extensions 2017-04-05 21:02:09 +02:00
Jorrit Boekel 82fe426214 Hardklor and kronik datatypes for proteomics 2017-04-05 20:38:10 +02:00
Gildas Le Corguillé c9f602d434 Update datatypes_conf.xml.sample 
Oups, I did it again :)

Just add the sniffer for the mzData datatype
 2017-03-31 12:18:00 +02:00
Nicola Soranzo 3ed60db5ce Merge branch 'release_17.01' into dev 
Conflicts:
	lib/galaxy/tools/deps/container_resolvers/__init__.py
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
 2017-03-22 01:27:10 +00:00
Daniel Blankenberg 376212eff9 Fix for uploading rdata datasets when explicitly declaring datatype. 
Now that ext's are forced to be all lowercase, you cannot upload a dataset with any uppercase characters in the extension.

TODO: An additional fix directly for the upload tool/datatype widget should be pursued that will prevent these issues.
 2017-03-17 10:34:07 -04:00
Jorrit Boekel 01e1bc6f30 Added percolator proteomics datatypes for input and output 2017-03-10 11:09:14 +01:00
Greg Von Kuster a7ec0c8579 Add datatypes for soon coming PlantTribes Galaxy tools. 2017-03-02 13:17:35 -05:00
lecorguille 99397fad74 add the mzData datatype 2017-02-24 13:54:52 +01:00
Björn Grüning d9b36176a8 Merge pull request #3580 from jj-umn/patch-5 
Add d3_hierarchy subclass
 2017-02-11 00:21:51 +01:00
Nicola Soranzo ed52230952 Merge branch 'release_17.01' into dev 
Conflicts:
	config/datatypes_conf.xml.sample
 2017-02-10 15:31:43 +00:00
Nicola Soranzo f8dcae9536 Remove edam_format for Genbank from config/datatypes_conf.xml.sample 
This was preventing the loading of the datatype:

WARNING 2017-02-10 11:07:05,162 Cannot specify edam_format without setting subclass to True, skipping datatype.

Bug introduced in commit c36fbebb44 .

Also backport commit 5657a8b809 from dev.
 2017-02-10 11:53:28 +00:00
Jim Johnson 0815e6b881 Add d3_hierarchy subclass 
This is to support Unipept API tool and visualization:   https://github.com/unipept/unipept-visualizations
The unipept visualization would only apply to the d3_hierarchy of json datasets.
 2017-02-08 11:01:16 -06:00
Nate Coraor 5657a8b809 Display the genbank file type in upload 2017-02-07 15:14:19 +11:00
John Chilton 1a463f1688 Pull build_sites out of datatypes conf. 
So deployers may modify these paths and stil use the default datatypes config.

This should speed up set_metadata also since each of these config files won't be loaded as part of that.
 2017-01-30 20:43:29 -05:00
Nicola Soranzo 7f232a25b5 Fix path to Smat datatype 2017-01-24 14:31:01 +00:00
John Chilton e74ca27dbf Revert "Markdown datatype support." 2017-01-11 21:48:09 -05:00
John Chilton a87feb11ff Merge pull request #3145 from mvdbeek/fastqgz 
Support for gzipped fastq formats
 2017-01-11 21:18:22 -05:00
John Chilton ca40f984b0 Markdown datatype support. 
With test tools demonstrating HTML and Markdown outputs from tools.

Implements #3396 as part of the Qiime hackathon.
 2017-01-10 15:51:08 -05:00
John Chilton f358d14670 Merge pull request #3379 from bgruening/dmnddb 
Add diamond database as datatype
 2017-01-09 13:19:21 -05:00
Bérénice Batut 0518cbf02e Add sniffer for dmnd extension 2017-01-05 16:37:12 +01:00
Thomas Wollmann b28051a886 fixed typo 2017-01-05 14:59:08 +01:00
Thomas Wollmann e0e2d6da7e added nrrd datatype 2017-01-05 14:56:00 +01:00
ThomasWollmann a870ac887c added STL datatype (#2679) 
* added STL datatype

* added image support to rstudio IE

* added image support to jupyter IE

* changed boolean to lower case

* lint

* lint

* revert file extension refactoring

* upgraded numpy-stl

* Update constructive_solid_geometry.py

added additional check to refine stl sniffer

* Update constructive_solid_geometry.py

* removed stl sniffer

* cleanup of dependencies

* revert file extension refactoring

* upgraded numpy-stl

* Update constructive_solid_geometry.py

added additional check to refine stl sniffer

* Update constructive_solid_geometry.py

* removed stl sniffer

* cleanup of dependencies

* lint
 2017-01-05 11:36:35 +01:00
Thomas Wollmann f46d8ad739 harmonised the use of capital and small letters 2017-01-03 17:04:28 +01:00
Thomas Wollmann 47e0d5d810 added hamatsu sub datatypes 2017-01-02 11:30:29 +01:00
Thomas Wollmann f4eadd71fd harmonised the use of capital and small letters 2017-01-02 11:27:00 +01:00
Thomas Wollmann 88e838c587 added tiff subtypes 2017-01-02 11:25:23 +01:00
Thomas Wollmann 7588e9df3d added image datatypes 2017-01-02 11:08:52 +01:00
Thomas Wollmann 968b97a0ac harmonised the use of capital and small letters 2017-01-02 11:06:30 +01:00
Björn Grüning 5f0a4131df Add diamond database 2017-01-01 18:02:08 +01:00
Nicola Soranzo 43075015dd Merge pull request #3339 from erasche/genbank 
Genbank datatype
 2016-12-19 22:45:16 +00:00
Eric Rasche c36fbebb44 genbank datatype 2016-12-19 20:25:04 +00:00
Delphine-L f4070ba981 Syntax cleaning 2016-12-16 15:07:26 -05:00
Delphine-L 27673f5e08 Addition of Genome fasta file loading in local IGV instance, and addition of fai format and fasta to fai converter 2016-12-16 13:39:51 -05:00
Greg Von Kuster 86447eced8 Add support for ESTScan scores matrices (smat) data type 2016-12-02 14:36:05 -05:00