Re: [galaxy-dev] galaxy-dev] format="input"
I put a patch for lib/galaxy/workflow/modules.py in: https://bitbucket.org/galaxy/galaxy-central/issue/582/output-format_source-not-supported-in On Thu, Jun 9, 2011 at 11:24 AM, Peter Cock wrote: > On Thu, Jun 9, 2011 at 8:39 AM, Peter Cock > wrote: > > > > Thanks for this, I can think of several of my own tools where this > > will work much more cleanly than the current solution using > > and . > > > > There is still a bit of work needed: > https://bitbucket.org/galaxy/galaxy-central/issue/582 > #582 output format_source not supported in workflow editor > > Peter > > P.S. I found your original email on this approach, > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-February/004334.html > ___ 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"
On Thu, Jun 9, 2011 at 8:39 AM, Peter Cock wrote: > > Thanks for this, I can think of several of my own tools where this > will work much more cleanly than the current solution using > and . > There is still a bit of work needed: https://bitbucket.org/galaxy/galaxy-central/issue/582 #582 output format_source not supported in workflow editor Peter P.S. I found your original email on this approach, http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-February/004334.html ___ 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] format="input"
Hi and thanks to you both ! Jim : I tryed your solution and it works just fine ! Peter : thanks for the advice, I'll support only sff/fastq as inputs you're right it makes think easier ! Jerome Peter Cock a écrit : On Wed, Jun 8, 2011 at 4:36 PM, Mariette wrote: Hi everyone, I'm facing a little problem ... Any ideas ? thx, I don't know what kind of tool you are working on, but personally I'd consider dropping support for FASTA+QUAL and try and work with either SFF or FASTQ only. It makes so many things easier. 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/ ___ 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"
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. no yes (qual['add'] == 'yes') On 6/9/11 2:39 AM, Peter Cock wrote: On Wed, Jun 8, 2011 at 9:59 PM, Jim Johnson wrote: It went into galaxy-central: $ hg log -pr 5082 changeset: 5082:a86e1fa82a89 user:Kanwei Li 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 and. Regards, 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"
On Wed, Jun 8, 2011 at 9:59 PM, Jim Johnson wrote: > > It went into galaxy-central: > > $ hg log -pr 5082 > changeset: 5082:a86e1fa82a89 > user: Kanwei Li > 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 and . Regards, 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
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 Johnson wrote:
I added an attribute "format_source" (analogous to metadata_source)
to the 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
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Re: [galaxy-dev] format="input"
On Wed, Jun 8, 2011 at 4:36 PM, Mariette wrote: > Hi everyone, > > I'm facing a little problem ... > Any ideas ? > thx, I don't know what kind of tool you are working on, but personally I'd consider dropping support for FASTA+QUAL and try and work with either SFF or FASTQ only. It makes so many things easier. 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"
On Wed, Jun 8, 2011 at 9:26 PM, Jim Johnson wrote: > I added an attribute "format_source" (analogous to metadata_source) > to the 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"
I added an attribute "format_source" (analogous to metadata_source) to the tag to deal with that kind of issue: see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax qual_file != None JJ Hi everyone, I'm facing a little problem ... I have the following input : and the following output: qual_file != None 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 ___ 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/
[galaxy-dev] format="input"
Hi everyone, I'm facing a little problem ... I have the following input : label="Quality reads file (if input is a fasta)" /> and the following output: qual_file != None 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 ___ 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/
