Daniel Blankenberg 377c2427a7 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. ...

Allow most MAF tools to allow limiting of output species. MAF tools which do not allow species limiting include Extract Pairwise MAF blocks, MAF Coverage stats, and Filter MAF blocks by Size.

The functionality of Filter MAF blocks by Species and Filter MAF blocks by Size is now available in Filter MAF by specified attributes. Unfortunately tests are still not able to be written for the Filter MAF by specified attributes tool.

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

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genebed_maf_to_fasta.xml

Add a new metadata type of Metadata Files.

2008-10-22 13:49:22 -04:00

interval2maf_pairwise.xml

Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.

2008-07-23 15:27:39 -04:00

interval2maf.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

interval2maf.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

interval_maf_to_merged_fasta.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

interval_maf_to_merged_fasta.xml

Add a new metadata type of Metadata Files.

2008-10-22 13:49:22 -04:00

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

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.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

Separate framework and tool environments.

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

maf_limit_size.xml

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

maf_limit_to_species.py

Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.

2008-04-25 13:04:55 +00:00

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

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_stats.py

Add a new metadata type of Metadata Files.

2008-10-22 13:49:22 -04:00

maf_stats.xml

Add a new metadata type of Metadata Files.

2008-10-22 13:49:22 -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

merging from central

2008-12-02 10:55:17 -05:00

maf_to_bed.py

Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.

2008-04-25 13:04:55 +00:00

maf_to_bed.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_fasta_concat.py

Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.

2008-04-25 13:04:55 +00:00

maf_to_fasta_multiple_sets.py

Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.

2008-04-25 13:04:55 +00:00

maf_to_fasta.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