New try :
${os.path.join( $input.extra_files_path, 'first_component_file.xxx' )}
${os.path.join( $input.extra_files_path, 'second_component_file.yyy')}
With this, I can see my tool takes as parameters :
myTool path/to/first_component_file.xxx path/to/second_component_file.yyy
This sounds great, isn't it ?
But I have now a message quoting the ''os.path.join'' line, and saying
"mauvaise substitution" which means "bad substitution".
(First why isn't it in English ? Does it mean it's not a Galaxy problem ?)
So I generated a new composite file, made of 2 components files, named exactly
as the "metadata.base_name" is set.
I used this two component files as an input in my other tool, and now I no
longer have this message !
That meansGalaxy wants the components files' name to be the same as the
"metadata.base_name" , if I understood well... So if user want to change the
name, it sure will fail...
How to fix this problem ?
Furthermore, it doesn't completely work. I think my tool thinks there is two
parameters instead of only one, when seeing the two paths for my components
files. I don't know how to fix it either...
Any ideas ?
Thank you for your attention,
Marine
________________________________
De : Ross <ross.laza...@gmail.com>
À : Marine Rohmer <marine.roh...@yahoo.fr>
Cc : "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Envoyé le : Vendredi 15 juin 2012 12h40
Objet : Re: Re : Composite output with self-declarated datatypes
Hi Marine,
Other people may have better ideas, but the way I've always done it is to
ensure that the tool knows how to find the input files inside the
extra_files_path because that's easy to pass.
If $i is the name of data parameter = composite file chosen from the user
history (ie a data input on your form), then you can pass it to the script as
(eg)
--extra_files_path "$i.extra_files_path"
You might also find
--base_name "$i.metadata.base_name"
handy sometimes for naming outputs
I hope this helps.
On Fri, Jun 15, 2012 at 7:29 PM, Marine Rohmer <marine.roh...@yahoo.fr> wrote:
Update : Now my tool creates a html composite output, made of 2 outputs .xxx
and .yyy.
>I've added the "def get_mime(self)" function in the python file describing all
>my formats, and now it works.
>When I run my tool and click on the eye symbol, I can see a html page with
>links to download the two component files.
>
>I thought everything was now going perfect, but when I try to use this
>composite output as an input in another tool I've added, this other tool can't
>open it.... Which makes sense to me, since the other tool needs both of the
>component files, and not an html input.
>
>So I wonderedhow to change the html composite output into the two component
>files ?
>I've tried to retrieve them in a bash wrapper with :
>
>component=""
>HTML_FILE="$1"
>for i in HTML_FILE
> do component="$i"
>done
>
>But with a simple "echo $component" test, I get "HTML_FILE" as a result, and
>not one of the component file.
>
>So is there any specified thing to do to recover the component files of a
>composite file ?
>
>Best regards,
>
>Marine
>
>
>
>
>
>>>>
>
>
>
>________________________________
>
>De : Ross <ross.laza...@gmail.com>
>À : Marine Rohmer <marine.roh...@yahoo.fr>
>Envoyé le : Mercredi 13 juin 2012 10h50
>
>Objet : Re: [galaxy-dev] Re : Composite output with self-declarated datatypes
>
>
>
>Look at your xml.
>Output_name is a text parameter - it doesn't have any paths It's certainly not
>a new output file Galaxy will create or an existing composite object - so it
>quite correctly complains about not having a files_path or extra_files_path
>
>
>
>On Wed, Jun 13, 2012 at 6:34 PM, Marine Rohmer <marine.roh...@yahoo.fr> wrote:
>
>Hi Ross,
>>
>>Thank you so much for your answer !
>>
>>I've changed my command line in myTool.xml as followed :
>>
>> <command> path/to/myTool-wrapper.sh
>>'$output_name.files_path/$output_name.metadata.base_name' $input_file
>> </command>
>>
>>But I still have the same error message, with "files_path" instead of
>>"extra_files_path" :
>>
>>
>>NotFound: cannot find 'files_path' while searching for
>>'output_name.files_path'
>>Well I'm going to grep those files as you said, and see if it can help me...
>>
>>Thank you again,
>>
>>Marine
>>
>>>>>
>>
>>
>>
>>________________________________
>> De : Ross <ross.laza...@gmail.com>
>>À : Marine Rohmer <marine.roh...@yahoo.fr>
>>Envoyé le : Mercredi 13 juin 2012 6h44
>>Objet : Re: [galaxy-dev] Re : Composite output with self-declarated datatypes
>>
>>
>>Marine,
>>Sorry to hear you're having problems - composite objects definitely do
>>work but they are definitely not simple or properly documented.
>>
>>I don't really have time to figure out exactly what the problem is but
>>one very obvious error message
>>
>>NotFound: cannot find 'extra_files_path' while searching for
>>'output_name.extra_files_path'
>>
>>is telling you that a new output file does not have an
>>extra_files_path at job submission.
>>
>>Try output_name.files_path - why it differs is something I do not
>>understand but I've learned to live with....
>>
>>If you grep for files_path in your tool/*/*.xml files, you'll find
>>lots of examples of tools using files_path and extra_files_path
>>(mostly html files) and studying those working examples might be
>>useful in getting your code to work?
>>
>>cheers...
>>
>>
>>On Tue, Jun 12, 2012 at 6:24 PM, Marine
Rohmer <marine.roh...@yahoo.fr> wrote:
>>> Hi,
>>>
>>> Maybe my message was not understandable enough. I really need your help, so
>>> I'll try to be more concise :
>>>
>>> How do I make a composite output from 2 datatypes that I have declared
>>> myself ?
>>> I've followed the "Composite Datatypes" wiki but it seems that I've missed
>>> 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
>>>
>>>
>>>
>>>
>>> ________________________________
>>> De : Marine Rohmer <marine.roh...@yahoo.fr>
>>> À : "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
>>> Envoyé le : Vendredi 8 juin 2012 15h15
>>> Objet : Composite output with self-declarated datatype
>>>
>>> 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 !
>>
>>
>>
>
>
>
>--
>Ross Lazarus MBBS MPH;
>Associate Professor, Harvard Medical School;
>Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>
>
>
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;___________________________________________________________
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