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 components are ".xxx" and ".yyy".
I've declared the datatype ".xxx", ".yyy" and ".composite" in the
datatypes_conf.xml file, and written the required python files . Now, ".xxx",
".yyy" and ".composite" appear in Get Data's "file format" .
These are my files :
In datatype_conf.xml :
<datatype extension="xxx" type="galaxy.datatypes.xxx:xxx" mimetype="text/html"
display_in_upload = "True" subclass="True"/>
<datatype extension="yyy" type="galaxy.datatypes.yyy:yyy"
mimetype="application/octet-stream" display_in_upload = "True" subclass="True"
/>
<datatype extension="composite" type="galaxy.datatypes.composite:Composite"
mimetype="text/html" display_in_upload="True"/>
xxx.py (summarized) :
import logging
from metadata import MetadataElement
from data import Text
log = logging.getLogger(__name__)
class xxx(Text):
file_ext = "xxx"
def __init__( self, **kwd ):
Text.__init__( self, **kwd )
yyy.py (summarized) :
import logging
from metadata import MetadataElement
from data import Text
log = logging.getLogger(__name__)
# yyy is a binary file, don't know what to put instead of "Text". "Binary" and
"Bin" don't work.
class yyy(Text):
file_ext = "yyy"
def __init__( self, **kwd ):
Text.__init__( self, **kwd )
composite.py (summarized) :
import logging
from metadata import MetadataElement
from data import Text
log = logging.getLogger(__name__)
class Composite(Text):
composite_type = 'auto_primary_file'
MetadataElement( name="base_name", desc="base name for all transformed
versions of this index dataset", default="your_index", readonly=True,
set_in_upload=True)
file_ext = 'composite'
def __init__( self, **kwd ):
Text.__init__( self, **kwd )
self.add_composite_file( '%s.xxx', description = "XXX file",
substitute_name_with_metadata = 'base_name')
self.add_composite_file( '%s.yyy', description = "YYY file",
substitute_name_with_metadata = 'base_name', is_binary = True )
Atfer having read Composite Datatypes in the wiki, my myTool.xml looks like :
<tool id="my tool">
<command> path/to/crac-index-wrapper.sh
${os.path.join( $output_name_yyy.extra_files_path, '%s.yyy')}
${os.path.join( $output_name_xxx.extra_files_path, '%s.xxx' )} $input_file
</command>
<inputs>
<param name="output_name" type="text" value ="IndexOutput" label="Output
name"/>
<param name="input_file" type="data" label="Source file" format="fasta"/>
</inputs>
<outputs>
<data format="ssa" name="output_name_ssa"
from_work_dir="crac-index_output.ssa" label="CRAC-index: ${output_name}.ssa">
</data>
<data format="conf" name="output_name_conf"
from_work_dir="crac-index_output.conf" label="CRAC-index: ${output_name}.conf">
</data>
</outputs>
</tool>
I have 2 main problems :
When I upload a xxx file via "Get Data", there's no problem. However, when I
upload a yyy file (the binary one),history bloc rests eternally blue
("uploading dataset") , even for a small file.
The second problem is that I want my tool to only generate the .composite file
on the history, and not each of .xxx and .yyy.
. But when I run my tool I still have 2 outputs displayed in the history : one
for xxx and one for yyy. Furthermore, neither of them work, and I have the
following message :
path/to/myTool-wrapper.sh: 6: path/to/myTool-wrapper.sh.sh: cannot create
/home/myName/work/galaxy-dist/database/files/000/dataset_302_files/%s.yyy.xxx:
Directory nonexistent
path/to/myTool-wrapper.sh: 6: path/to/myTool-wrapper.sh: cannot create
/home/myName/work/galaxy-dist/database/files/000/dataset_302_files/%s.yyy.yyy:
Directory nonexistent
path/to/myTool-wrapper.sh: 11: path/to/myTool-wrapper.sh: Syntax error:
redirection unexpected
So I've checked manually in /home/myName/work/galaxy-dist/database/files/000/
and there's only "dataset_302.dat", an empty file.
(And whatsmore, I don't understand why I get in the message "%s.yyy.xxx" and
"%s.yyy.yyy" instead of "%s.yyy" and "%s.xxx" ...)
Then I've looked the example of rgenetics.xml, and tried to change the command
line and the output :
<tool id="my tool">
<command> path/to/myTool-wrapper.sh
'$output_name.extra_files_path/$output_name.metadata.base_name' $input_file
</command>
<inputs>
<param name="output_name" type="text" value ="IndexOutput" label="Output
name" />
<param name="input_file" type="data" label="Source file" />
</inputs>
<outputs>
<data format="html" name="output" label="myTool: ${output_name}.html"
metadata_source="input_file"/>
</outputs>
</tool>
This gave me :
Traceback (most recent call last):
File "/home/myName/work/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
59, in run_job
job_wrapper.prepare()
File "/home/myName/work/galaxy-dist/lib/galaxy/jobs/__init__.py", line 429,
in prepare
self.command_line = self.tool.build_command_line( param_dict )
File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line 1971,
in build_command_line
command_line = fill_template( self.command, context=param_dict )
File "/home/myName/work/galaxy-dist/lib/galaxy/util/template.py", line 9, in
fill_template
return str( Template( source=template_text, searchList=[context] ) )
File
"/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
line 1004, in __str__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1339157051_58_87978.py",
line 83, in respond
NotFound: cannot find 'extra_files_path' while searching for
'output_name.extra_files_path'
So now I don't know which way is the one to follow : the first one inspired by
the example in the wiki, or the second one inspired by rgenetics.xml. And
what's wrong with it...
I will really appreciate any suggestion !
Best regards,
Marine___________________________________________________________
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