galaxy

genebed_maf_to_fasta.xml

Upgrade to Cheetah 2.2.2

2009-11-10 13:47:34 -05:00

interval2maf_pairwise.xml

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

interval2maf.py

Fix limiting species in interval2maf tool.

2009-09-29 21:47:59 -04:00

interval2maf.xml

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

interval_maf_to_merged_fasta.py

First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.

2009-09-04 10:40:16 -04:00

interval_maf_to_merged_fasta.xml

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

maf_by_block_number.py

Allow workflows that contain tools that had parameters added to them after the workflow was created to be edited. Workflows containing tools with added parameters can still not be run until after they are edited and saved. Default values are provided in the workflow building mode.

2009-02-04 14:55:45 -05:00

maf_by_block_number.xml

Allow workflows that contain tools that had parameters added to them after the workflow was created to be edited. Workflows containing tools with added parameters can still not be run until after they are edited and saved. Default values are provided in the workflow building mode.

2009-02-04 14:55:45 -05:00

maf_filter.py

First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.

2009-09-04 10:40:16 -04:00

maf_filter.xml

Allow workflows that contain tools that had parameters added to them after the workflow was created to be edited. Workflows containing tools with added parameters can still not be run until after they are edited and saved. Default values are provided in the workflow building mode.

2009-02-04 14:55:45 -05:00

maf_limit_size.py

First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.

2009-09-04 10:40:16 -04:00

maf_limit_size.xml

First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.

2009-09-04 10:40:16 -04:00

maf_limit_to_species.py

First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.

2009-09-04 10:40:16 -04:00

maf_limit_to_species.xml

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

maf_reverse_complement.py

Allow workflows that contain tools that had parameters added to them after the workflow was created to be edited. Workflows containing tools with added parameters can still not be run until after they are edited and saved. Default values are provided in the workflow building mode.

2009-02-04 14:55:45 -05:00

maf_reverse_complement.xml

Add a MAF to Interval converter that produces a set of intervals with sequence data.

2009-09-17 11:47:37 -04:00

maf_split_by_species.py

First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.

2009-09-04 10:40:16 -04:00

maf_split_by_species.xml

Fix heading for Example 2 in maf_split_by_species onscreen tool help.

2009-09-04 11:08:10 -04:00

maf_stats.py

Fix reporting number of regions processed in MAF Stats tool.

2009-09-30 14:06:06 -04:00

maf_stats.xml

First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.

2009-09-04 10:40:16 -04:00

maf_thread_for_species.py

Separate framework and tool environments.

2008-04-11 20:11:21 +00:00

maf_thread_for_species.xml

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

maf_to_bed_code.py

Better approach to altering initial content of output dataset if necessary. The upload tool will now call the data type's groom_output_dataset() method ( a better name than before_setting_metadata since it is not related to metadata ). This will now also run on the cluster.

2009-12-08 11:46:13 -05:00

maf_to_bed.py

Fix MAF to BED tool. This tool should be rewritten to not use a code file, but instead use one of the standard ways to create additional outputs, similar to how maf_to_interval functions.

2009-11-30 15:33:45 -05:00

maf_to_bed.xml

Fix MAF to BED tool. This tool should be rewritten to not use a code file, but instead use one of the standard ways to create additional outputs, similar to how maf_to_interval functions.

2009-11-30 15:33:45 -05:00

maf_to_fasta_concat.py

First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.

2009-09-04 10:40:16 -04:00

maf_to_fasta_multiple_sets.py

First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.

2009-09-04 10:40:16 -04:00

maf_to_fasta.xml

Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.

2011-02-28 12:16:28 -05:00

maf_to_interval.py

Add a MAF to Interval converter that produces a set of intervals with sequence data.

2009-09-17 11:47:37 -04:00

maf_to_interval.xml

Update tool tests for MAF to interval tool

2010-03-09 14:29:17 -05:00

vcf_to_maf_customtrack.py

Support for VCFv4.0 and misc VCF fixes [Brad Chapman]

2010-08-03 10:43:32 -04:00

vcf_to_maf_customtrack.xml

Update vcf_to_mafcustomtrack tool to enforce a minimum of one dataset to be selected.

2010-07-14 12:18:24 -04:00