appliance tutorial: problem with planemo tool_init

[martenson]

This is in the .ova image

Am I doing something wrong here @jmchilton ?

ubuntu@packer-virtualbox-iso-1466017992:~/Desktop/tools$ planemo tool_init --force \
>                     --macros \
>                     --id 'seqtk_seq' \
>                     --name 'Convert to FASTA (seqtk)' \
>                     --requirement seqtk@1.0-r68 \
>                     --example_command 'seqtk seq -a 2.fastq > 2.fasta' \
>                     --example_input 2.fastq \
>                     --example_output 2.fasta \
>                     --test_case \
>                     --help_from_command 'seqtk seq'
Tool written to seqtk_seq.xml
Macros file macros.xml already exists, assuming  it has relevant planemo-generated definitions.
Copying test-file 2.fastq
cp '2.fastq' 'test-data'
Copying test-file None
cp 'None' 'test-data'
cp: cannot stat 'None': No such file or directory

ubuntu@packer-virtualbox-iso-1466017992:~/Desktop/tools$ ls
2.fasta  2.fastq  macros.xml  seqtk_seq.xml  test-data

[jmchilton]

Yup - that is broken. I'll push a new planemo with a fix asap.

[martenson]

I think this is fixed by https://github.com/galaxyproject/planemo/commit/b1f9e930c4119347eefd0c6d61ee339548463b82