do
file_without_extension=${myfile%%.xxx}
done
myTool -i $file_without_extension
This works perfectly !
Thank you Ross for your attention, your help was precious !
Marine
________
De : Ross
À : Marine Rohmer
Cc : "galaxy-dev@lists.bx.psu.edu"
Envoyé
mponents
files. I don't know how to fix it either...
Any ideas ?
Thank you for your attention,
Marine
De : Ross
À : Marine Rohmer
Cc : "galaxy-dev@lists.bx.psu.edu"
Envoyé le : Vendredi 15 juin 2012 12h40
Objet : Re: Re : Composite output
my tool a path to the two files I need, within
>>>path/to/database/files/000/dataset_375.files.
>>>So I thought to use metadata.base_name but this obviously gives the default
>>>name of the two files, and not the one user gave while running the tool on
>>>Gala
mponent" test, I get "HTML_FILE" as a result, and
not one of the component file.
So is there any specified thing to do to recover the component files of a
composite file ?
Best regards,
Marine
>>>
De : Ross
À : Marine Rohmer
En
something...
My composite datatype appears well in "file format" from Get Data's upload file
section, but when I run my tool, I have 2 outputs which are the components of
my primary datatype, instead of only one output.
Best regards,
Marine
_____
Hi everyone,
I'm trying to add a tool which generates 2 files, that I will call ".xxx" (a
text file) and ".yyy" (a binary file) . Both files are needed to use the
result of my tool with an other tool I've added.
So I wanted to create a composite datatype , that I will call ".composite",
whose
Tool
-i = $genome_index
-r = $input
-k = $kmer_length
/path/to/indexEcoli
path/to/indexHuman
Regards,
Marine
De : Hans-Rudolf Ho
Regards,
Marine
____
De : Hans-Rudolf Hotz
À : Marine Rohmer
Cc : "galaxy-dev@lists.bx.psu.edu"
Envoyé le : Mercredi 30 mai 2012 11h42
Objet : Re: [galaxy-dev] Error executing tool: cannot find 'database'
Hi Marine
Could you please provid
Hi everyone,
I'm trying with all my best to add an NGS tool into my local Galaxy instance.
I've added my tool in tool_conf.xml, and made a XML file with all the
, etc... I think it's pretty ok, and everything is correctly
displayed on the Galaxy interface.
However, when I execute my tool, Ga
