Nicola Soranzo
f69c06b6cf
Merge pull request #1033 from scholtalbers/wig_to_bigwig_error_msg
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wig_to_bigwig: Add error message for wrongly formatted data
2015-11-05 18:37:35 +00:00
Jelle Scholtalbers
4908a5bab6
wig_to_bigwig: Add error message for wrongly formatted data
2015-11-05 19:15:51 +01:00
Nicola Soranzo
69cda48690
Remove remaining references to galaxy.eggs . flake8 some files in tools/ .
2015-10-26 19:29:13 +00:00
Daniel Blankenberg
120ec61264
Fix command quoting and remove size from text input for Cut tool.
2015-10-14 10:11:21 -04:00
Björn Grüning
6430b9c4e8
Update documentation for the gff_filter_by_attribute tool
2015-10-05 18:43:36 +02:00
Nicola Soranzo
22d4a1d8c3
dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.
2015-05-15 12:40:52 +01:00
peterjc
aafd2d0a51
Add sorting option to Count1 (tools/filters/uniq.xml)
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When using this tool to produce a tally table, often want to
have the most common entries listed first - rather than the
sort order coming from the values being counted.
2015-03-13 16:43:02 -04:00
peterjc
fc58d3d781
Fix trailing space removal
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I had a test case which showed the problem, I just over looked it.
The input file species_assignment.tabular now includes more trailing
space examples columns 2, 3 and 4 to make this visually clearer at
first glance (previously the single trailing space example was
too easily overlooked).
2015-03-13 16:43:02 -04:00
peterjc
1317cf8a84
Remove trailing comma space in uniq.py stdout
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$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2.tabular -c 2 -d T
Count of unique values in c2,
$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2c3.tabular -c 2,3 -d T
Count of unique values in c2, c3,
becomes:
$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2.tabular -c 2 -d T
Count of unique values in c2
$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2c3.tabular -c 2,3 -d T
Count of unique values in c2, c3
2015-03-13 16:43:01 -04:00
peterjc
9f18034805
Do not remove spaces in Count1 (tools/filters/uniq.xml), with tests
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Also sets the tool version for the first time, using 1.0.1.
$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2.tabular -c 2 -d T
Count of unique values in c2,
$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2c3.tabular -c 2,3 -d T
Count of unique values in c2, c3,
2015-03-13 16:43:01 -04:00
peterjc
fce2184e5b
Make tool version explicit (Job runner would assume 1.0.0)
2015-03-09 15:21:48 +00:00
Martin Cech
709abedcb4
Merged in anton/galaxy-central-anton (pull request #539 )
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Initial tweaks to tool_conf.xml sample and one of the tools.
2014-11-11 12:26:45 -05:00
Nicola Soranzo
fbcf3e2bbc
Make stripping and condensing optional.
2014-10-28 16:57:49 +01:00
Nicola Soranzo
526c2507d7
dos2unix
2014-10-28 12:21:00 +01:00
Anton Nekrutenko
873d1f455c
uniq.xml edited online with Bitbucket
2014-10-23 16:42:15 +00:00
Dannon Baker
9d85ca9e23
Switch to_json_string/from_json_string in galaxy/tools.
2014-09-09 10:06:35 -04:00
Björn Grüning
b9389cc76d
Add empty_field validator to gtf2bedgraph.xml
2014-06-27 22:21:37 +00:00
Dannon Baker
a6b6879f12
Reorder imports post-PR 403.
2014-06-09 10:53:00 -04:00
Saket Choudhary
769a1d4f49
PEP8 fixes, close find handles for 'convert delimiters to tab' tool
2014-06-09 11:56:06 +05:30
Dannon Baker
559ecb4ec8
Remove dependency on simplejson; convert everything over to using the json module in the python standard library.
2014-01-10 07:29:05 -05:00
John Chilton
53cb37aed3
Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines.
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As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html ).
There are still two copies.
2013-11-07 12:56:48 -05:00
John Chilton
73206460d6
Backed out changeset 9532e80796ec
2013-11-07 13:02:22 -05:00
John Chilton
4a3820ef58
Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines.
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As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html ).
There are still two copies.
2013-11-07 12:56:48 -05:00
Dannon Baker
63e9ba7f27
Merged in ghuls/galaxy-central/sort (pull request #172 )
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Fix sorting of numbers in scientific notation.
2013-08-07 13:33:27 -04:00
Jeremy Goecks
bc27b54627
Add semicolon to the list of delimiters in the 'Convert delimiters to whitespace tool'.
2013-06-21 11:59:13 -04:00
Gert Hulselmans
f0ee6b578e
Fix sorting of numbers in scientific notation.
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The -n option of sort can't handle numbers in scientific notation.
The -g option of sort can handle those numbers correctly.
2013-05-28 15:48:45 +02:00
Aysam Guerler
0e0f2605fa
grep/select tool: fixed tab-delimiter matching for GNU version of grep
2013-04-02 15:18:22 -04:00
Jeremy Goecks
6a69ebc669
Merge in next-stable
2013-03-21 12:19:45 -04:00
Jeremy Goecks
bacf200965
Add support for column ranges to Cut tool. Thank to John Chilton for this code.
2013-03-21 12:19:14 -04:00
Aysam Guerler
109f6c8316
tool tip fix for fastq summary and sorter
2013-03-19 11:50:03 -04:00
Aysam Guerler
e26eb773aa
Provide backwards compatibility for sorter
2013-03-15 17:29:29 -04:00
Aysam Guerler
8cd17848ad
sort: update log to browser
2013-03-08 12:10:19 -05:00
Aysam Guerler
bdbd21f250
sort: preserves comments in sorted output
2013-03-08 11:52:37 -05:00
Joachim Jacob
3dd11e95d8
Adjusted trimming tool to include negative positions. Modified help and test.
2013-01-30 10:38:58 +01:00
Jeremy Goecks
9719bed6f9
Enable BedGraph to be used as input to wig-to-bigwig tool.
2013-01-24 17:06:51 -05:00
Dave Clements
f706f34948
Replaced "query" with "dataset" in a number of tool definition XML files.
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I got tired of coming across "query" when doing workshops.
2013-01-14 16:13:54 -08:00
Jeremy Goecks
e23d56219b
Fix output definition for GTF filter by attribute values list/
2012-12-04 13:42:09 -05:00
Ross Lazarus
6a892b3555
Fix parameters for fastqc to work properly with bam and with a contaminants file
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Been b0rken for a long time - probably not much used..
2012-10-26 16:00:13 +11:00
Jeremy Goecks
9fabf5dfbe
Add feature/attribute name indexing framework to converters. Provide full text indexing for GFF attributes.
2012-08-16 16:32:00 -04:00
Scott McManus
e069425ab9
Removed offending code from last checkin - sorry for the foul-up
2012-08-07 13:35:39 -04:00
Scott McManus
92915592f9
Added minor changes, including model accessors, for cancelling PBS tasks
2012-08-05 23:45:11 -04:00
Jeremy Goecks
df28aec040
Full and proper sorting for GTF datasets: sort by, in order, transcript_id, chrom, and start.
2012-05-24 13:26:48 -04:00
Daniel Blankenberg
7c930f1c92
Tool help updates.
2011-11-14 13:26:29 -05:00
Daniel Blankenberg
9f9e55f320
Update sff extractor to version 0.2.10.
2011-10-20 16:38:14 -04:00
Daniel Blankenberg
940bb8d738
Some random lines tool tweaks.
2011-09-25 13:27:14 -04:00
Daniel Blankenberg
09e8a94a5a
Rewrite random lines tool. Does two passes through input file: first pass determines line offsets/count, offsets are randomly removed, second pass writes out lines by seeking to remaining offsets. The random seed can now be optionally specified.
2011-09-23 13:49:33 -04:00
Daniel Blankenberg
727ce45cbf
Fix tabs in secure_hash_message_digest.xml.
2011-09-09 12:15:27 -04:00
Daniel Blankenberg
9017c6fbd8
Add tool for calculating Secure Hashes / Message Digests of a dataset using the user selected algorithms.
2011-09-09 12:01:43 -04:00
Anton Nekrutenko
d2d6956108
Patch from Peter Cock (bug534) for cut tool to ignore commented lines.
2011-06-08 17:17:11 -04:00
Jeremy Goecks
1d03c82144
Enable GFF filter attributes tool to accept arbitrary conditions.
2011-05-05 16:51:56 -04:00
Nicola Soranzo