galaxy

phastOdds

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

extract_genomic_dna_code.py

Added exception handling, additional test and some code cleanup for extract_genomic_dna script.

2008-01-28 13:41:46 +00:00

extract_genomic_dna.py

Better error handling in extract_genomic_dna tool, behavior doesn't change so new version not necessary.

2008-02-05 20:13:07 +00:00

extract_genomic_dna.xml

add the new version of the extract_genomic_dna.xml

2008-01-29 18:27:06 +00:00

extract_GFF_Features.py

Modified error handling in 'Extract GFF features' tool. The tool will display a simple error message in place of stack trace.

2008-02-05 17:00:40 +00:00

extract_GFF_Features.xml

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

extractAxt_wrapper.pl

Remove last references to /depot/data1/cache.

2007-01-03 19:36:07 +00:00

extractAxt_wrapper.xml

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

fasta-subseq-wrapper_code.py

Extracting Genomic DNA can now result in an interval file with the

2007-09-25 16:12:37 +00:00

fasta-subseq-wrapper.pl

Extracting Genomic DNA can now result in an interval file with the

2007-09-25 16:12:37 +00:00

fasta-subseq-wrapper.xml

Add a validator that checks if the value for a dataset's metadata item exists in a file and column.

2008-01-17 18:41:45 +00:00

liftOver_wrapper_code.py

Adding liftOver tool. Test section is commented as the functinal test module doesn't handle multiple outputs yet. I've downloaded liftOver mapping files from UCSC for all the genomes for which we have sequences. I've added a function in get_ucsc_scores.pl file (which contains functions to fetch sequences and alignments) to fetch liftOver mappings too.

2008-01-17 19:24:34 +00:00

liftOver_wrapper.py

Adding liftOver tool. Test section is commented as the functinal test module doesn't handle multiple outputs yet. I've downloaded liftOver mapping files from UCSC for all the genomes for which we have sequences. I've added a function in get_ucsc_scores.pl file (which contains functions to fetch sequences and alignments) to fetch liftOver mappings too.

2008-01-17 19:24:34 +00:00

liftOver_wrapper.xml

Adding liftOver tool. Test section is commented as the functinal test module doesn't handle multiple outputs yet. I've downloaded liftOver mapping files from UCSC for all the genomes for which we have sequences. I've added a function in get_ucsc_scores.pl file (which contains functions to fetch sequences and alignments) to fetch liftOver mappings too.

2008-01-17 19:24:34 +00:00

twoBitToFa

Tool to extract genomic DNA from unassembled sequences.

2007-05-29 19:50:25 +00:00

twoBitToFa_wrapper.py

add version to the extract genomic dna tool.

2008-01-24 21:02:53 +00:00

twoBitToFa_wrapper.xml

Add a validator that checks if the value for a dataset's metadata item exists in a file and column.

2008-01-17 18:41:45 +00:00