This tool is now failing, for all versions, at usegalaxy.org and usegalaxy.eu.
New workaround for End-users
- Use this alternative tool:
Samtools fastx extract FASTA or FASTQ from alignment files
- Located in the tool panel grouping
SAM/BAM on most Galaxy servers.
- Find it using the tool search function at the top of the left tool panel.
- Tool is also available in the Workflow editor tool panel.
- If running your own Galaxy server, the tool may need to be installed from the ToolShed.
The alternative tool above may be more useful anyway. It has expanded input/output options, including but not limited to: 1) input
cram data, coordinate sorted or not, 2) output
fastqsanger (or the appropriate
fastq sub-type), 3) output a compressed or uncompressed version of the data, 4) output paired-end reads in different ways (R1 only, R2 only, both R1+R2 in two distinct datasets, or R1+R2 interleaved in a single dataset), and 5) output has the appropriate datatype, assigned directly by the tool. Meaning, there is no need use
Configure Output to re-assign the datatype when used in a workflow, and no need to re-assign/re-detect the datatype when used directly in a History.
Allowing Galaxy to assign the datatype will ensure that it is correct and matches the actual content of the user-specified output type. This avoids introducing unintentional mismatched “datatype” metadata problems that can lead to downstream tool errors.