hello
I am using new galaxy user and i integrate the tool inside the galaxy but when i execute the tool it will show the error
Error executing tool: No dataset upload groups were found.
please any one can tell me solution on this.
Hi,
please read the Galaxy Tool Config wiki page, or have a look at the thousands of other tools out there. The 'type="file"' does not exist. You need to use 'type="data"'. It is usually a good start to search for a similar wrapper and start from there.
Cheers,
Bjoern
Hii,
Thanks Bjoern for the answer it help me now i face the another error when upload a .bam file from getdata->Upload file in
galaxy.
Error is.
tool error
An error occurred with this dataset:
Unable to finish job
can you please tell me solution on this error how i upload a .bam file.
Dataset 143: Small_test.bam
The Galaxy framework encountered the following error while attempting to run the tool:
Traceback (most recent call last):
File "/home/plus91/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 118, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/plus91/galaxy-dist/lib/galaxy/jobs/__init__.py", line 959, in finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation
File "/home/plus91/galaxy-dist/lib/galaxy/datatypes/binary.py", line 244, in set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: Samtools-htslib-API: bam_index_build2() not yet implemented
Aborted (core dumped)
This is error has been accour when upload .bam file
See Error after upload bam file for this problem (a bug in samtools)
Can you please add your XML code to the question. Otherwise we can not help you. Thanks!
This the XML code :
<tool id="softsearch" name="softsearch"><description>for structure variation</description>
<command interpreter="perl"> /home/data/2.4/src/SoftSearch.pl -b $bam_file -f $fasta_file </command>
<inputs>
<param name="bam_file" type="file" format="bam" label="BAM Files" />
<param name="fasta_file" type="file" format="fasta" label="FASTA Files" help="OR" />
</inputs>
<outputs>
<data format="tabular" name="out_file1" />
</outputs>
<help>
</help>
</tool>
I also face with error after upload the file
Error executing tool: FileToolParameter cannot be persisted
please tell me solution on this.