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8dd7a9e570746df9c1fc35607cdeca072599b348
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70 Commits
Author SHA1 Message Date
Dannon Baker 03351d2a9f Apply black to tools as well 2022-02-03 09:12:13 -05:00
Nicola Soranzo 9d74bba7fb Drop support for retired Python 3.5 
Upgrade syntax using `pyupgrade --py36-plus` .

Manually drop several `six` imports.

Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
 2020-10-07 11:52:13 +01:00
Marius van den BeekandSergey Golitsynskiy 61bdd76f35 Update tools/plotting/bar_chart.py 
Co-Authored-By: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
 2020-02-06 16:28:52 +01:00
mvdbeek 2fe556959d Fix string module use 2020-02-06 16:18:28 +01:00
Nicola Soranzo f865e8359f Deprecate size attribute of <param/> and remove it from tools 
Also:
- dos2unix test/functional/tools/for_workflows/head.xml
- Single-quote text and data params in `<command/>`
- Remove deprecated `interpreter` attribute of `<command />`
 2018-09-10 11:34:37 +01:00
mvdbeek 6c7203b83d py3: Fix qual_stats_boxplot 2018-09-05 14:22:00 +02:00
Nicola Soranzo 9b4de72ca6 Fix all E722 errors and ignore E741 
Introduced in flake8 3.5.0
Fix import order.
 2017-10-24 11:29:09 +01:00
Nicola Soranzo 21b44bf348 Fix all E201 and E202 style errors 
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
 2017-08-17 11:35:39 +01:00
John Chilton 45bf7ad8c4 Make requirement tags in bar_chart.xml functional with default dependency resolver. 
I'm not sure if we need to update the version since previously these tags were purely for documentation and had no functional purpose.

xref this comment https://github.com/galaxyproject/galaxy/pull/3444#issuecomment-273909855 from @bgruening
 2017-01-19 17:05:53 -05:00
Nicola Soranzo 39da6c3278 Fix the remaining 2180 flake8 errors in tools/ . 2016-02-10 18:46:03 +00:00
Nicola Soranzo 8703f3bd9e Remove unused files. 2016-02-10 17:35:31 +00:00
Nicola Soranzo 341a6cf760 Use requirements of type="package" instead of deprecated "binary". 2015-05-15 12:43:15 +01:00
Nicola Soranzo 22d4a1d8c3 dos2unix of tools/ directory. Some whitespace and PEP-8 fixes. 2015-05-15 12:40:52 +01:00
peterjc fce2184e5b Make tool version explicit (Job runner would assume 1.0.0) 2015-03-09 15:21:48 +00:00
John Chilton 8db7eed06a Add annotated citations various tools. 2014-08-06 09:41:38 -04:00
Dave Bouvier 35bc12d769 Migrate tools from the distribution to the tool shed. 2014-07-28 11:58:52 -04:00
John Chilton 892912c02d Merged in abrenner/galaxy-central (pull request #215) 
histogram2 - RPY requires R - missing from requirements tag

Thanks for the contribution!
 2013-10-16 22:12:40 -05:00
Dave Bouvier b0efe4ddea Migrate tools from the distribution to the tool shed, including but not limited to samtools and fastx_toolkit tools. 2013-09-26 10:05:00 -04:00
Adam Brenner 35d32232d4 histogram2.xml python module rpy requires R package. 2013-09-12 18:36:20 +00:00
Jeremy Goecks 9a5679c37c Use mako template in tool help so that dynamic image paths can be used. Fixes #141 2012-08-07 09:40:51 -04:00
Daniel Blankenberg a6ecae74fd Minor tool help updates. 2011-09-08 10:34:56 -04:00
Ross Lazarus d53c3e984f Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository 
This is a backout of commit 5765
 2011-07-06 09:44:56 +10:00
Ross Lazarus 86b55bb0c0 branch merge 2011-07-05 12:40:43 +10:00
Nate Coraor a221548e8f An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix. 2011-03-08 11:17:57 -05:00
Nate Coraor e3f970a36f Use lines_diff on the pdf outputs of various R-based tools. 2011-03-03 12:21:44 -05:00
Guruprasad Anada ff7e8fe2e0 Fixed functional tests for the following tools: histogram, estimate indel rates, compute q-values, kernel pca. 2011-02-22 12:37:06 -05:00
Nate Coraor 409f149aa4 Fix for the histogram tool for the "'x' must be numeric" error experienced by some local installations. Thanks, Jim Johnson. 2011-02-03 15:52:44 -05:00
Dannon Baker 349d3a07bb First pass standardizing to 'dataaset' from 'query'. 2011-01-27 13:46:20 -05:00
Kanwei Li 2d0b8eb830 Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141 2010-12-14 14:22:13 -05:00
Daniel Blankenberg 8e42a241d6 Enhance histogram tool to allow plotting as frequency/counts. 2010-12-09 15:39:58 -05:00
Anton Nekrutenko 2763d08d86 Modified help section and help tags to ease paremeter selection by the user 2010-12-03 09:57:45 -05:00
Daniel Blankenberg 00306e15ed Make boxplot tool respect exit codes when determining job errors: makes e.g. 'Could not find/open font when opening font "arial", using internal non-scalable font' a non-fatal warning. Add version attribute to gnuplot requirement tag. 2010-03-22 11:06:40 -04:00
Daniel Blankenberg 4cb98d8b5f Add gnuplot requirement tag to boxplot tool. 2010-02-23 19:54:54 -05:00
Daniel Blankenberg 8082c6f36f Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid. 
Tools include:
	FASTQ Groomer convert between various FASTQ quality formats
	Combine FASTA and QUAL into FASTQ
	FASTQ joiner on paired end reads
	FASTQ splitter on joined paired end reads
	FASTQ to FASTA converter
	FASTQ Summary Statistics by column
	Filter FASTQ reads by quality score and length
	FASTQ Trimmer by column
	Manipulate FASTQ reads on various attributes
	Boxplot of quality statistics (Generic, with outliers)
 2010-02-23 16:48:07 -05:00
Nate Coraor 65d3ad47cd Fix from Assaf Gordon for Cheetah syntax errors in the Bar Chart tool. 2010-02-08 10:00:30 -05:00
Guruprasad Anada ae3e0763b9 Updating histogram functional test output, which had changed as a result of R version upgrade. 2009-12-14 15:17:13 -05:00
Greg Von Kuster eca5a69f9f Update the output test dataset for the XY_Plot_1 tool due to a new version of R, and update the tool version so the functional test will pass. 2009-12-10 09:18:49 -05:00
Daniel Blankenberg f92b25d2f5 Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142. 
Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles.

Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes  (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes.

Future Enhancement:
Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
 2009-12-07 10:19:41 -05:00
Guruprasad Anada bcd0192709 Fix bar chart output format. 2009-08-03 16:38:27 -04:00
Guruprasad Anada 167ce59b29 Bug fixes for histogram liftover and grouping tools. 2009-05-29 11:07:18 -04:00
Guruprasad Anada fa533faa95 push changesets to security from central 2009-03-05 13:09:02 -05:00
Guruprasad Anada ebeece6204 Adding a tiny fix to scatter plot tool. 2009-03-05 13:02:17 -05:00
Anton Nekrutenko 43891dced2 updated bar charter to use png instead of pdf 2009-01-22 12:06:29 -05:00
Greg Von Kuster 5331dee076 Add functioal test baseline support for the repeat construct, more work needed ( e.g., multiple repeat elements, refresh_on_change when the input to be refreshed is within a repeat construct ). Added functional tests for some tools that use this construct. 2008-11-10 14:22:01 -05:00
Guruprasad Anada 9887101d60 Fix for scatterplot.py: Handling an uncaught exception. 2008-09-08 14:36:37 -04:00
Greg Von Kuster 04e0834500 Revert 2715. 2008-06-04 13:02:15 +00:00
Greg Von Kuster dedc7278a1 Requires config change, temporary files are now created in a configurable location - affects many tools. 2008-06-03 20:29:54 +00:00
Nate Coraor f53cb1d7f1 Added tool dependencies to xml. 2008-04-25 19:40:16 +00:00
Greg Von Kuster 1580ed8260 Functional tests will now properly handle output datasets in pdf format. Added functional tests for histogram and scatterplot. Fixed a bug where temporary files was not removed if functional test failed. 2008-04-04 14:45:29 +00:00
Greg Von Kuster af3b0669aa Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4. 2008-03-28 15:24:50 +00:00