[galaxy-dev] Re : Composite output with self-declarated datatypes
I finally have found a solution to my problem.
In fact my tool needs in its command line the name of the files without the
extension, (example : only "fileName", instead of "fileName.xxx fileName.yyy")
and that is what mattered in my opinion. Note : the name of the two files is
exactly the same, only the extension changes.
So I write in my bash wrapper (I'm not really comfortable with Python) :
#!/bin/bash
# Recovering the parameters from the xml file
INDEX_INPUT="$1"
# Getting the file name without the extension
for myfile in /$INDEX_INPUT/*.xxx
do
file_without_extension=${myfile%%.xxx}
done
myTool -i $file_without_extension
This works perfectly !
Thank you Ross for your attention, your help was precious !
Marine
De : Ross
À : Marine Rohmer
Cc : "galaxy-dev@lists.bx.psu.edu"
Envoyé le : Samedi 16 juin 2012 4h16
Objet : Re: Re : Composite output with self-declarated datatypes
Marine,
It seems that the files your tool needs are in the extra_files_path and you
just have to figure out how to get at them for processing.
From my experience, it is trivial to make this work with a wrapper script in
Python.
Given a directory listing of the passed in extra_files_path, you can easily
figure out which input is which.
It's probably possible with bash but it would definitely not be my personal
preference.
A general purpose scripting language like python would probably make it easier
but if you insist on bash, I am sure you already have enough information to get
it to work.
On Sat, Jun 16, 2012 at 2:08 AM, Marine Rohmer wrote:
New try :
>${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
>À : Marine Rohmer
>
>Cc : "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 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=""
>>
Re: [galaxy-dev] Re : Composite output with self-declarated datatypes
Marine,
It seems that the files your tool needs are in the extra_files_path and you
just have to figure out how to get at them for processing.
>From my experience, it is trivial to make this work with a wrapper script
in Python.
Given a directory listing of the passed in extra_files_path, you can easily
figure out which input is which.
It's probably possible with bash but it would definitely not be my personal
preference.
A general purpose scripting language like python would probably make it
easier but if you insist on bash, I am sure you already have enough
information to get it to work.
On Sat, Jun 16, 2012 at 2:08 AM, Marine Rohmer wrote:
> 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 :
> myToolpath/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 means Galaxy 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
> *À :* Marine Rohmer
> *Cc :* "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 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 wondered how 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
> *À :* Marine Rohmer
> *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 wrote:
>
> Hi Ross,
>
> Thank you so much for your answer !
>
>
[galaxy-dev] Re : Composite output with self-declarated datatypes
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
À : Marine Rohmer
Cc : "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 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 $component" test, I get "HTML_FILE" as a result, and
>not one of the component file.
>
>So is there any specified thing to do to recover the component files of a
>composite file ?
>
>Best regards,
>
>Marine
>
>
>
>
>
>>>>
>
>
>
>
>
>De : Ross
>À : Marine Rohmer
>Envoyé le : Mercredi 13 juin 2012 10h50
>
>Objet : Re: [galaxy-dev] Re : Composite output with self-declarated datatypes
>
>
>
>Look at your xml.
>Output_name is a text parameter - it doesn't have any paths It's certainly not
>a new output file Galaxy will create or an existing composite object - so it
>quite correctly complains about not having a files_path or extra_files_path
>
>
>
>On Wed, Jun 13, 2012 at 6:34 PM, Marine Rohmer wrote:
>
>Hi Ross,
>>
>>Thank you so much for your answer !
>>
>>I've changed my command line in myTool.xml as followed :
>>
>> path/to/myTool-wrapper.sh
>>'$output_name.files_path/$output_name.metadata.base_name' $input_file
>>
>>
>>But I still have the same error message, with "files_path" instead of
>>"extra_files_path" :
>>
>>
>>NotFound: cannot find 'files_path' while searching for
>>'output_name.files_path'
>>Well I'm going to grep those files as you said, and see if it can help me...
>>
>>Thank you again,
>>
>>Marine
>>
>>>>>
>>
>>
>>
>>
>> De : Ross
>>À : Marine Rohmer
>>Envoyé le : Mercredi 13 juin 2012 6h44
>>Objet : Re: [galaxy-dev] Re : Composite output with self-declarated datatype
[galaxy-dev] Re : Composite output with self-declarated datatypes
Thank you Ross for answering so fast, >>> >>>I've tried with "$i.extra_files_path". When I run my tool, it takes as >>>argument "path/to/database/files/000/dataset_375.files" which indeed is the >>>file that contains the two files I want. >>> >>>But I still have an error message "Cannot open file" . So I guess there is >>>something else to do to make my tool understand it has to take the two files >>>inside extra_files_path. That's what you wanted to say ? >>> >>>I thought about putting $i.extra_files_path in a variable "INPUT" in my bash >>>wrapper, and writting in the command line something like : >>>-option $INPUT/name_of_file_to_recover >>>instead of : >>>-option $INPUT >>>in order to give to 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 >>>Galaxy... >>> >>>Maybe I just miss a little thing, or I'm on a wrong way...? >>> De : Ross À : Marine Rohmer Cc : "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 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 $component" test, I get "HTML_FILE" as a result, and >not one of the component file. > >So is there any specified thing to do to recover the component files of a >composite file ? > >Best regards, > >Marine > > > > > >>>> > > > > > >De : Ross >À : Marine Rohmer >Envoyé le : Mercredi 13 juin 2012 10h50 > >Objet : Re: [galaxy-dev] Re : Composite output with self-declarated datatypes > > > >Look at your xml. >Output_name is a text parameter - it doesn't have any paths It's certainly not >a new output file Galaxy will create or an existing composite object - so it >quite correctly complains about not having a files_path or extra_files_path > > > >On Wed, Jun 13, 2012 at 6:34 PM, Marine Rohmer wrote: > >Hi Ross, >> >>Thank you so much for your answer ! >> >>I've changed my command line in myTool.xml as followed : >> >> path/to/myTool-wrapper.sh >>'$output_name.files_path/$output_name.metadata.base_name' $input_file >> >> >>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 >>À : Marine Rohmer >>Envoyé le : Mercredi 13 juin 2012 6h44 >>Objet : Re: [galaxy-dev] Re : Composite output with self-declarated datatypes
Re: [galaxy-dev] 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 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 wondered how 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 $component" test, I get "HTML_FILE" as a result, > and not one of the component file. > > So is there any specified thing to do to recover the component files of a > composite file ? > > Best regards, > > Marine > > > > > > > > -- > *De :* Ross > *À :* Marine Rohmer > *Envoyé le :* Mercredi 13 juin 2012 10h50 > > *Objet :* Re: [galaxy-dev] Re : Composite output with self-declarated > datatypes > > Look at your xml. > Output_name is a text parameter - it doesn't have any paths It's certainly > not a new output file Galaxy will create or an existing composite object - > so it quite correctly complains about not having a files_path or > extra_files_path > > > On Wed, Jun 13, 2012 at 6:34 PM, Marine Rohmer wrote: > > Hi Ross, > > Thank you so much for your answer ! > > I've changed my command line in myTool.xml as followed : > > path/to/myTool-wrapper.sh > '$output_name.files_path/$output_name.metadata.base_name' > $input_file > > > 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 > *À :* Marine Rohmer > *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 > 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 prima
[galaxy-dev] Re : Composite output with self-declarated datatypes
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 $component" test, I get "HTML_FILE" as a result, and not one of the component file. So is there any specified thing to do to recover the component files of a composite file ? Best regards, Marine >>> ____ De : Ross À : Marine Rohmer Envoyé le : Mercredi 13 juin 2012 10h50 Objet : Re: [galaxy-dev] Re : Composite output with self-declarated datatypes Look at your xml. Output_name is a text parameter - it doesn't have any paths It's certainly not a new output file Galaxy will create or an existing composite object - so it quite correctly complains about not having a files_path or extra_files_path On Wed, Jun 13, 2012 at 6:34 PM, Marine Rohmer wrote: Hi Ross, > >Thank you so much for your answer ! > >I've changed my command line in myTool.xml as followed : > > path/to/myTool-wrapper.sh >'$output_name.files_path/$output_name.metadata.base_name' $input_file > > >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 >À : Marine Rohmer >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 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 >> À : "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"
[galaxy-dev] Re : Composite output with self-declarated datatypes
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
À : "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 :
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 :
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' )} $input_file
I have 2 main problems :
When I upload a xxx file via "Get Data", there's no problem. However, when I
upload a yyy
file (the binary one),history bloc rests eternally blue ("uploading dataset")
, even for a small file.
The second problem is that I want my tool to only generate the .composite file
on the history, and not each of .xxx and .yyy.
. But when I run my tool I still have 2 outputs displayed in the history : one
for xxx and one for yyy. Furthermore, neither of them work, and I have the
following message :
path/to/myTool-wrapper.sh: 6: path/to/myTool-wrapper.sh.sh: cannot create
/home/myName/work/galaxy-dist/database/files/000/dataset_302_files/%s.yyy.xxx:
Directory nonexistent
path/to/myTool-wrapper.sh: 6: path/to/myTool-wrapper.sh: cannot create
/home/myName/work/galaxy-dist/database/files/000/dataset_302_files/%s.yyy.yyy:
Directory nonexistent
path/to/myTool-wrapper.sh: 11: path/to/myTool-wrapper.sh: Syntax error:
redirection unexpected
So I've checked manually in /home/myName/work/galaxy-dist/database/files/000/
and there's only "dataset_302.dat", an empty file.
(And whatsmore, I don't understand why I get in the message "%s.yyy.xxx" and
"%s.yyy.yyy" instead of "%s.yyy" and "%s.xxx" ...)
Then I've looked the example of rgenetics.xml, and tried to change the command
line and the output :
path/to/myTool-wrapper.sh
'$output_name.extra_files_path/$output_name.metadata.base_name' $input_file
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
