Re: [galaxy-dev] galaxy-dev] format=input
I added an example taken from trim.seqs.xml in the Mothur metagenomics
tool_suite to:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
The following will create datasets in the history panel, setting the output data type to
be the same as that of an input dataset named by the format_source attribute.
Note that a conditional name is not included, so 2 separate conditional blocks should not
contain parameters with the same name.
inputs
!-- fasta may be an aligned fasta that subclasses Fasta --
param name=fasta type=data format=fasta label=fasta - Sequences/
conditional name=qual
param name=add type=select label=Trim based on a quality file? help=
option value=nono/option
option value=yesyes/option
/param
when value=no/
when value=yes
!-- qual454, qualsolid, qualillumina --
param name=qfile type=data format=qual label=qfile - a quality file/
/when
/conditional
/inputs
outputs
data format_source=fasta name=trim_fasta label=${tool.name} on ${on_string}:
trim.fasta/
data format_source=qfile name=trim_qual label=${tool.name} on ${on_string}:
trim.qual
filter(qual['add'] == 'yes')/filter
/data
/outputs
On 6/9/11 2:39 AM, Peter Cock wrote:
On Wed, Jun 8, 2011 at 9:59 PM, Jim Johnsonjohns...@umn.edu wrote:
It went into galaxy-central:
$ hg log -pr 5082
changeset: 5082:a86e1fa82a89
user:Kanwei Likan...@gmail.com
date:Thu Feb 17 15:35:07 2011 -0500
summary: Add a format_source attribute to the ToolConfig output data
element [JJ Johnson]. Closes #470
...
And I should have put an example in:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
Oh right - better late than never ;)
On the bright side because this commit was a while ago, it has
already been included in the stable Galaxy releases.
Thanks for this, I can think of several of my own tools where this
will work much more cleanly than the current solution using
change_format andwhen.
Regards,
Peter
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[galaxy-dev] format=input
Hi everyone,
I'm facing a little problem ...
I have the following input :
param name=input type=data format=sff,fasta,fastq label=454
reads /
param name=qual_file type=data format=qual optional=true
label=Quality reads file (if input is a fasta) /
and the following output:
data name=output format=input label=${tool.name} on ${on_string}:
cleaned reads/
data name=out_qual format=qual label=${tool.name} on ${on_string}:
cleaned reads
filterqual_file != None/filter
/data
If I provide the tool a sff file, the output is sff, if I only provide a
fasta file and no qual file the output will be a fasta.
However if I provide a fasta+qual the output will be considered as qual
file even if it's a fasta file.
I don't get how it can mark my output file as a qual file knowing it's
not a valid input file format.
Any ideas ?
thx,
Jerome
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Re: [galaxy-dev] galaxy-dev] format=input
On Wed, Jun 8, 2011 at 9:26 PM, Jim Johnson johns...@umn.edu wrote: I added an attribute format_source (analogous to metadata_source) to the data tag to deal with that kind of issue: see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Where is the code to handle this? Maybe I missed the commit with all the recent activity. What happens if both format and format_source are given? I would hope an error - which means the wiki is misleading in that format is listed as required. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] galaxy-dev] format=input
It went into galaxy-central: $ hg log -pr 5082 changeset: 5082:a86e1fa82a89 user:Kanwei Li kan...@gmail.com date:Thu Feb 17 15:35:07 2011 -0500 summary: Add a format_source attribute to the ToolConfig output data element [JJ Johnson]. Closes #470 diff -r 885f04ae671e -r a86e1fa82a89 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Feb 17 14:48:53 2011 -0500 +++ b/lib/galaxy/tools/__init__.py Thu Feb 17 15:35:07 2011 -0500 @@ -249,10 +249,11 @@ (format, metadata_source, parent) -def __init__( self, name, format=None, metadata_source=None, +def __init__( self, name, format=None, format_source=None, metadata_source=None, parent=None, label=None, filters = None, actions = None ): self.name = name self.format = format +self.format_source = format_source self.metadata_source = metadata_source self.parent = parent self.label = label @@ -559,6 +560,7 @@ output = ToolOutput( data_elem.get(name) ) output.format = data_elem.get(format, data) output.change_format = data_elem.findall(change_format) +output.format_source = data_elem.get(format_source, None) output.metadata_source = data_elem.get(metadata_source, ) output.parent = data_elem.get(parent, None) output.label = util.xml_text( data_elem, label ) diff -r 885f04ae671e -r a86e1fa82a89 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Thu Feb 17 14:48:53 2011 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Thu Feb 17 15:35:07 2011 -0500 @@ -244,6 +244,12 @@ ext = output.format if ext == input: ext = input_ext +if output.format_source is not None and output.format_source in inp_data: +try: +ext = inp_data[output.format_source].ext +except Exception, e: +pass + #process change_format tags if output.change_format: if params is None: And I should have put an example in: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax On 6/8/11 3:32 PM, Peter Cock wrote: On Wed, Jun 8, 2011 at 9:26 PM, Jim Johnsonjohns...@umn.edu wrote: I added an attribute format_source (analogous to metadata_source) to thedata tag to deal with that kind of issue: see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Where is the code to handle this? Maybe I missed the commit with all the recent activity. What happens if both format and format_source are given? I would hope an error - which means the wiki is misleading in that format is listed as required. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
