Hi,
I am trying to integrate some tools into Galaxy but I have encountered some difficulties in attempting to understand how the XML tool definition works exactly ... despite the XML tag documentation available at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax .
Imagine a case where the presence of certain arguments depends on: - its value e.g we don't want to include it if its value is undefined - other arguments' values e.g if the value of x is greater than the y value we don't want to include the x argument on the command line
How can I specify it using the XML definition?
A simplified case:
A tool needs arguments A and B or an input file F
We want to propose two modes to configure it - [1] a basic mode where we can graphically set A and B values using fields such as text value... - [2] an advanced mode where we can specify a file containing complex configuration to upload
tool command line:
for [1] tool.py -A arg1 -B arg2 [2] tool.py -F confile
I don't want to include the -F command line argument if -A and -B are defined I currently manage these cases using wrappers...quite boring
Where can we find: - advanced documentation for XML definition - commented advanced examples - related discussions
Best regards
Seb
[sorry for the bad english]
Hi Sébastien,
You can use regular Cheetah syntax in our xml configs, like such:
#if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
#else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
#end if
The above was extracted from the wiki page you linked, although we don't seem to have explicit Cheetah definitions
-Kanwei
2010/7/9 Sébastien HARISPE harispe.sebastien@gmail.com:
Hi, I am trying to integrate some tools into Galaxy but I have encountered some difficulties in attempting to understand how the XML tool definition works exactly ... despite the XML tag documentation available at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax . Imagine a case where the presence of certain arguments depends on:
- its value e.g we don't want to include it if its value is undefined
- other arguments' values e.g if the value of x is greater than the y value we don't want to include the x argument on the command line How can I specify it using the XML definition? A simplified case: A tool needs arguments A and B or an input file F We want to propose two modes to configure it
- [1] a basic mode where we can graphically set A and B values using fields
such as text value...
- [2] an advanced mode where we can specify a file containing complex
configuration to upload tool command line: for [1] tool.py -A arg1 -B arg2 [2] tool.py -F confile
I don't want to include the -F command line argument if -A and -B are defined I currently manage these cases using wrappers...quite boring
Where can we find: - advanced documentation for XML definition - commented advanced examples - related discussions
Best regards Seb [sorry for the bad english] _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi,
Thanks for your reply Li, I was under the impression that Cheetah syntax was reserved for conditional parameters use.
Cheetah is not really simple to debug (Tricks ?).
Can someone help me with the following command definition ?
<command interpreter="python"> #set $cmd = '' #if $chromo != '' #$cmd = ' $cmd -c $chromo ' #end if #if $start != '' #$cmd = ' $cmd -s $chromo ' #end if #if $end != '' #$cmd = ' $cmd -e $end ' #end if #if $DB != '' #$cmd = ' $cmd -d $DB ' #end if #if $conf_file != '' #$cmd = ' $cmd -f $conf_file ' #end if # ucsc.py $cmd -o $out -l $log -p $log_C -f -u $useConf </command>
Error:
/usr/bin/python: can't find '__main__.py' in '/xxxxx/galaxy/galaxy_dist/tools/'
Is there a forum or another way to found old related posts ?
Best regards
2010/7/9 Kanwei Li kanwei@gmail.com
Hi Sébastien,
You can use regular Cheetah syntax in our xml configs, like such:
#if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
#else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
#end if
The above was extracted from the wiki page you linked, although we don't seem to have explicit Cheetah definitions
-Kanwei
2010/7/9 Sébastien HARISPE harispe.sebastien@gmail.com:
Hi, I am trying to integrate some tools into Galaxy but I have encountered
some
difficulties in attempting to understand how the XML tool definition
works
exactly ... despite the XML tag documentation available at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax . Imagine a case where the presence of certain arguments depends on:
- its value e.g we don't want to include it if its value is undefined
- other arguments' values e.g if the value of x is greater than the y
value we don't want to include the x argument on the command line How can I specify it using the XML definition? A simplified case: A tool needs arguments A and B or an input file F We want to propose two modes to configure it
- [1] a basic mode where we can graphically set A and B values using
fields
such as text value...
- [2] an advanced mode where we can specify a file containing complex
configuration to upload tool command line: for [1] tool.py -A arg1 -B arg2 [2] tool.py -F confile
I don't want to include the -F command line argument if -A and -B are defined I currently manage these cases using wrappers...quite boring
Where can we find: - advanced documentation for XML definition - commented advanced examples - related discussions
Best regards Seb [sorry for the bad english] _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Sébastien,
If you look in tools/ngs_rna/tophat_wrapper.xml you will see a good example similar to what you are trying to do. Instead of generating a long "cmd" string you can simply have if statements to naturally add more arguments to the command. You also have a typo (use $chromo twice instead of $start). Also I don't think the ucsc.py line should have a #.
We don't have a forum, but you can search our mailing archives in google: "site:http://lists.bx.psu.edu/pipermail/ cheetah".
-K
2010/7/12 Sébastien HARISPE harispe.sebastien@gmail.com:
Hi, Thanks for your reply Li, I was under the impression that Cheetah syntax was reserved for conditional parameters use. Cheetah is not really simple to debug (Tricks ?). Can someone help me with the following command definition ? <command interpreter="python"> #set $cmd = '' #if $chromo != '' #$cmd = ' $cmd -c $chromo ' #end if #if $start != '' #$cmd = ' $cmd -s $chromo ' #end if #if $end != '' #$cmd = ' $cmd -e $end ' #end if #if $DB != '' #$cmd = ' $cmd -d $DB ' #end if #if $conf_file != '' #$cmd = ' $cmd -f $conf_file ' #end if # ucsc.py $cmd -o $out -l $log -p $log_C -f -u $useConf </command>
Error: /usr/bin/python: can't find '__main__.py' in '/xxxxx/galaxy/galaxy_dist/tools/' Is there a forum or another way to found old related posts ? Best regards
2010/7/9 Kanwei Li kanwei@gmail.com
Hi Sébastien,
You can use regular Cheetah syntax in our xml configs, like such:
#if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
#else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
#end if
The above was extracted from the wiki page you linked, although we don't seem to have explicit Cheetah definitions
-Kanwei
2010/7/9 Sébastien HARISPE harispe.sebastien@gmail.com:
Hi, I am trying to integrate some tools into Galaxy but I have encountered some difficulties in attempting to understand how the XML tool definition works exactly ... despite the XML tag documentation available at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax . Imagine a case where the presence of certain arguments depends on:
- its value e.g we don't want to include it if its value is undefined
- other arguments' values e.g if the value of x is greater than the y value we don't want to include the x argument on the command line How can I specify it using the XML definition? A simplified case: A tool needs arguments A and B or an input file F We want to propose two modes to configure it
- [1] a basic mode where we can graphically set A and B values using
fields such as text value...
- [2] an advanced mode where we can specify a file containing complex
configuration to upload tool command line: for [1] tool.py -A arg1 -B arg2 [2] tool.py -F confile
I don't want to include the -F command line argument if -A and -B are defined I currently manage these cases using wrappers...quite boring
Where can we find: - advanced documentation for XML definition - commented advanced examples - related discussions
Best regards Seb [sorry for the bad english] _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Li,
Thanks for your support, tophat_wrapper.xml was a very good example and I can now build my command line using Cheetah syntax.
We really appreciate the developers community involvement to help users understand how to use galaxy.
Have a good day
2010/7/12 Kanwei Li kanwei@gmail.com
Hi Sébastien,
If you look in tools/ngs_rna/tophat_wrapper.xml you will see a good example similar to what you are trying to do. Instead of generating a long "cmd" string you can simply have if statements to naturally add more arguments to the command. You also have a typo (use $chromo twice instead of $start). Also I don't think the ucsc.py line should have a #.
We don't have a forum, but you can search our mailing archives in google: "site:http://lists.bx.psu.edu/pipermail/ cheetah".
-K
2010/7/12 Sébastien HARISPE harispe.sebastien@gmail.com:
Hi, Thanks for your reply Li, I was under the impression that Cheetah syntax
was
reserved for conditional parameters use. Cheetah is not really simple to debug (Tricks ?). Can someone help me with the following command definition ?
<command interpreter="python"> #set $cmd = '' #if $chromo != '' #$cmd = ' $cmd -c $chromo ' #end if #if $start != '' #$cmd = ' $cmd -s $chromo ' #end if #if $end != '' #$cmd = ' $cmd -e $end ' #end if #if $DB != '' #$cmd = ' $cmd -d $DB ' #end if #if $conf_file != '' #$cmd = ' $cmd -f $conf_file ' #end if # ucsc.py $cmd -o $out -l $log -p $log_C -f -u $useConf </command>
Error: /usr/bin/python: can't find '__main__.py' in '/xxxxx/galaxy/galaxy_dist/tools/' Is there a forum or another way to found old related posts ? Best regards
2010/7/9 Kanwei Li kanwei@gmail.com
Hi Sébastien,
You can use regular Cheetah syntax in our xml configs, like such:
#if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
#else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
#end if
The above was extracted from the wiki page you linked, although we don't seem to have explicit Cheetah definitions
-Kanwei
2010/7/9 Sébastien HARISPE harispe.sebastien@gmail.com:
Hi, I am trying to integrate some tools into Galaxy but I have encountered some difficulties in attempting to understand how the XML tool definition works exactly ... despite the XML tag documentation available at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax . Imagine a case where the presence of certain arguments depends on:
- its value e.g we don't want to include it if its value is undefined
- other arguments' values e.g if the value of x is greater than the
y
value we don't want to include the x argument on the command line How can I specify it using the XML definition? A simplified case: A tool needs arguments A and B or an input file F We want to propose two modes to configure it
- [1] a basic mode where we can graphically set A and B values using
fields such as text value...
- [2] an advanced mode where we can specify a file containing complex
configuration to upload tool command line: for [1] tool.py -A arg1 -B arg2 [2] tool.py -F confile
I don't want to include the -F command line argument if -A and -B are defined I currently manage these cases using wrappers...quite boring
Where can we find: - advanced documentation for XML definition - commented advanced examples - related discussions
Best regards Seb [sorry for the bad english] _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev@lists.galaxyproject.org
-
Kanwei Li -
Sébastien HARISPE