Jennifer Hillman-Jackson
Jennifer Hillman-Jackson
**Tool version**: https://toolshed.g2.bx.psu.edu/view/devteam/picard/00fe2ff64467 **Problem**: Tool attempts to execute using all selected inputs in one job, then fails. If run on one dataset at a time (same datasets that fail with...
For a use case, please see this Biostars post: https://biostar.usegalaxy.org/p/13232/ Moved from Trello: https://trello.com/c/zxhZPTxA
Maybe not a true bug, but unexpected input requirements that are not defined on the tool form. The "Random" function requires that the input BAM/SAM is coordinate sorted. Meaning that...
This has been very confusing for users. Could we modify the tool so that pileup is assigned? BTW- when converting tabular to pileup, the UI consistantly produces a metadata error...
There is no "end coordinate". Example of a 6-column pileup dataset: > 1.Chrom 2.Start 3.Base 4 5 6 > chr1 2299 G 1 ^~. C > chr1 2300 T 1...
Details reported in dataset info field: > Log: tool progress > Log: tool progress > Unknown option: vcfinput > Usage: > table_annovar.pl [arguments] > > ``` > Optional arguments: >...
The tool does not load in the Tool Shed UI and this error is given to the user: The tool does not load on usegalaxy.org or https://test.galaxyproject.org - captured here...
Example usage: https://biostar.usegalaxy.org/p/14780/ Group = Use the same logic as the Group function - meaning, one output row per distinct key. Filter: Use same logic as "Filter by column" but...
The purpose of this option "unsorted" is unclear. From what I can tell, the dataset is unchanged. Could we clarify what the purpose of the option is in the tool...
Tools: https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_all_fasta/fb744a070bee https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_dbkeys_all_fasta/bca4c608408c Problem: chrM is not ordered for GATK Also see: https://biostar.usegalaxy.org/p/13903/#14444