Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum
 You'll need to white list the semi-colon which Galaxy has replaced as 
a security precaution (user free text can be exploited). See sanitizer 
here: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter



Thanks: adding :

   sanitizer
  valid initial=string.printable
 remove value=apos;/
/valid
 /sanitizer


fixed the probem.

 Could you confirm if the environment variable is being set now?

Hum the variable is not set , I've changed command to

command![CDATA[echo  JVARKITDIR=\$JVARKITDIR 
expression=${expression}   /tmp/error7.txt  java -cp 
\$JVARKITDIR/commons-jexl-2.1.1.jar:\$JVARKITDIR/commons-logging-1.1.1.jar:\$JVARKITDIR/htsjdk-1.129.jar:\$JVARKITDIR/snappy-java-1.0.3-rc3.jar:\$JVARKITDIR/vcffilterjs.jar 
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e 
'${expression}' -o ${output} ${input}  2 /tmp/error7.txt ]]



here is the content of tmp/error7.txt

$ cat /tmp/error7.txt
JVARKITDIR= expression=variant!=null;
Error: Could not find or load main class 
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS




P.
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Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 2:43 PM, John Chilton jmchil...@gmail.com wrote:

 Also not need to escape $__tool_directory__  (so use
 $__tool_directory__ instead of \$__tool_directory__).

 -John

If this was unclear, $VAR in the command XML fragment
is taken to be a Python variable available within the Cheetah
parser. Typically this would be one of your usr-set parameters.

Escaping the dollar as \$VAR in the XML fragment means
it is ignored by the Cheetah parser and becomes $VAR
in the command line string, meaning an environment
variable.

Using bash syntax you can insert a default value, e.g.
many tools use something like -t \${GALAXY_SLOTS:-8}
which would default to 8 threads even in older Galaxy
instances where the $GALAXY_SLOTS environment
variable wasn't setup.

Peter
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Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum

On 02/26/2015 03:43 PM, John Chilton wrote:

Sorry I wasn't clear about that - it hasn't reached galaxy-dist yet -
you can download the latest snapshot of 15.03 release (I believe it is
running on usegalaxy.org as of yesterday) via this link instead
https://bitbucket.org/galaxy/galaxy-central/get/release_15.03.zip.

Also not need to escape $__tool_directory__  (so use
$__tool_directory__ instead of \$__tool_directory__).

-John



thank you for your help John  Peter

hum... is there anything new with this version about tool.xml ?. I can 
see my tool in the right menu but the main page is blank (no input fields)


   127.0.0.1 - - [26/Feb/2015:16:09:07 +0200] GET
   /tool_runner?tool_id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   HTTP/1.1 200 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Ubuntu;
   Linux i686; rv:35.0) Gecko/20100101 Firefox/35.0
   127.0.0.1 - - [26/Feb/2015:16:09:17 +0200] GET
   /tool_runner?tool_id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   HTTP/1.1 200 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Ubuntu;
   Linux i686; rv:35.0) Gecko/20100101 Firefox/35.0
   127.0.0.1 - - [26/Feb/2015:16:09:27 +0200] GET
   /tool_runner?tool_id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   HTTP/1.1 200 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Ubuntu;
   Linux i686; rv:35.0) Gecko/20100101 Firefox/35.0
   127.0.0.1 - - [26/Feb/2015:16:09:28 +0200] GET
   /tool_runner?tool_id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   HTTP/1.1 200 - http://127.0.0.1:8080/; Mozilla/5.0 (X11; Ubuntu;
   Linux i686; rv:35.0) Gecko/20100101 Firefox/35.0


$ xmllint --format tools/jvarkit2/vcffilterjs.xml
?xml version=1.0?
tool hidden=false 
id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS 
version=1.0.0 name=vcffilterjs

  requirements
requirement type=binaryjava/requirement
  /requirements
  command![CDATA[echo dir=$__tool_directory__ .  /tmp/error7.txt 
 java -cp 
$__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.129.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcffilterjs.jar 
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e 
'${expression}' -o ${output} ${input}  2 /tmp/error7.txt ]]/command

  inputs
param format=vcf name=input type=data label=VCF input/
param name=expression type=text label=javascript expression
  sanitizer
valid initial=string.printable
  remove value='/
/valid
  /sanitizer
/param
  /inputs
  outputs
data format=vcf name=output/
  /outputs
  stdio
exit_code range=1:/
exit_code range=:-1/
  /stdio
  helpHelp/help
/tool

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Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum

On 02/26/2015 04:20 PM, John Chilton wrote:

Well - this version does feature Sam's complete rewrite of the front
end for tools - so things will be pretty different.

Oddly though your tool loaded for me - can you open up your JavaScript
console and let me know if there are any errors?


my bad, everything worked fine after... I opened the javascript console (?)

Ok, it works fine now !

Many thanks !

Pierre

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Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 1:35 PM, Pierre Lindenbaum
pierre.lindenb...@univ-nantes.fr wrote:
 You'll need to white list the semi-colon which Galaxy has replaced as a
 security precaution (user free text can be exploited). See sanitizer here:
 https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter


 Thanks: adding :

sanitizer
   valid initial=string.printable
  remove value=apos;/
 /valid
  /sanitizer


 fixed the probem.

Good.

 Could you confirm if the environment variable is being set now?

 Hum the variable is not set , ...

How was the tool installed into your Galaxy? Was it via a (local)
Tool Shed which would have processed the tool_dependencies.xml
file?

Or, have you manually added your tool XML to Galaxy by hand
(which is what I still do when developing a new tool)? In this
case you'd have to manually set the environment variable.
(I delay messing about with dependencies until after the tool
works locally, and then test them via the Test Tool Shed.)

Peter
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Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread John Chilton
Just to make sure - since it hasn't been explicitly stated - is this
tool being installed from the tool shed? The environment variable
setup in tool_dependencies.xml will only be available for tool shed
installs. You will also need a special requirement in your tool to
make it available
(https://github.com/bgruening/galaxytools/blob/master/augustus/augustus.xml#L6).

I consider this whole approach very heavy and not robust given that it
is explicitly tied to the tool shed. If there is any way you can
explicitly target the next release with your code there is a much
better solution to this problem - you can use $__tool_directory__ to
reference the directory tools are installed in
(https://bitbucket.org/galaxy/galaxy-central/commits/ddbe0d12bc86da406bb96213e23b8ddb273ed669).
It works for tool shed installations and tools just directly loaded
into Galaxy - it also doesn't require you to setup anything special in
tool_dependencies.xml or the requirements section. It is a cheetah
variable instead of a runtime environment variable so need to escape
the $ either.

If you are on an older version of Galaxy - the diff above is pretty
small - you should be possible to backport this enhancement locally
with minimal effort.

Hope this helps,

-John


On Thu, Feb 26, 2015 at 8:35 AM, Pierre Lindenbaum
pierre.lindenb...@univ-nantes.fr wrote:
 You'll need to white list the semi-colon which Galaxy has replaced as a
 security precaution (user free text can be exploited). See sanitizer here:
 https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter


 Thanks: adding :

sanitizer
   valid initial=string.printable
  remove value=apos;/
 /valid
  /sanitizer


 fixed the probem.

 Could you confirm if the environment variable is being set now?

 Hum the variable is not set , I've changed command to

 command![CDATA[echo  JVARKITDIR=\$JVARKITDIR
 expression=${expression}   /tmp/error7.txt  java -cp
 \$JVARKITDIR/commons-jexl-2.1.1.jar:\$JVARKITDIR/commons-logging-1.1.1.jar:\$JVARKITDIR/htsjdk-1.129.jar:\$JVARKITDIR/snappy-java-1.0.3-rc3.jar:\$JVARKITDIR/vcffilterjs.jar
 com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e '${expression}'
 -o ${output} ${input}  2 /tmp/error7.txt ]]


 here is the content of tmp/error7.txt

 $ cat /tmp/error7.txt
 JVARKITDIR= expression=variant!=null;
 Error: Could not find or load main class
 com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS



 P.

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Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum

On 02/26/2015 02:51 PM, John Chilton wrote:

Just to make sure - since it hasn't been explicitly stated - is this
tool being installed from the tool shed? The environment variable
setup in tool_dependencies.xml will only be available for tool shed
installs.


no, my future plan is to put it in the tool shed but for now, I'm just 
trying to make it run in my local instance of galaxy.


I'm sorry if that wasn't clear.


I've just downloaded the latest version of galaxy via 
https://bitbucket.org/galaxy/galaxy-dist/get/tip.zip ( 
galaxy-galaxy-dist-02ddea42faad.zip )

and re-tried.


I tried to print the variable $__tool_directory__ with the tool.xml below

but it's not defined

$ cat /tmp/error7.txt
dir= .
Error: Could not find or load main class 
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS



the xml:

   ?xml version=1.0?
   tool hidden=false
   id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   version=1.0.0 name=vcffilterjs
  requirements
requirement type=binaryjava/requirement
  /requirements

  command![CDATA[echo dir=\$__tool_directory__ . 
   /tmp/error7.txt  java -cp
   
\$__tool_directory__/commons-jexl-2.1.1.jar:\$__tool_directory__/commons-logging-1.1.1.jar:\$__tool_directory__/htsjdk-1.129.jar:\$__tool_directory__/snappy-java-1.0.3-rc3.jar:\$__tool_directory__/vcffilterjs.jar
   com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e
   '${expression}' -o ${output} ${input}  2 /tmp/error7.txt ]]/command
  inputs
param format=vcf name=input type=data label=VCF
   input/
param name=expression type=text label=javascript
   expression
sanitizer
 valid initial=string.printable
 remove value=apos;/
/valid
/sanitizer
/param
/inputs
  outputs
data format=vcf name=output/
/outputs
  stdio
exit_code range=1:/
exit_code range=:-1/
  /stdio
  help/help
   /tool


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Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Pierre Lindenbaum

Hi Peter,


i wrote the tool_dependencies.xml


   ?xml version=1.0?
   tool_dependency
package name=jvarkit version=1.0.0
install version=1.0.0
actions
action type=set_environment
environment_variable name=JVARKITDIR
   action=set_to$INSTALL_DIR/environment_variable
/action
/actions
/install
readme/readme
/package
   /tool_dependency




and updated vcffilterjs.xml


   ?xml version=1.0?
   tool hidden=false
   id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   version=1.0.0 name=vcffilterjs
  requirements
  requirement type=package version=1.0.0jvarkit/requirement
requirement type=binaryjava/requirement
  /requirements


  command![CDATA[java -cp
   
\$JVARKITDIR/commons-jexl-2.1.1.jar:\$JVARKITDIR/commons-logging-1.1.1.jar:\$JVARKITDIR/htsjdk-1.129.jar:\$JVARKITDIR/snappy-java-1.0.3-rc3.jar:\$JVARKITDIR/vcffilterjs.jar
   com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e
   '${expression}' -o ${output} ${input}  ]]/command
  inputs
param format=vcf name=input type=data label=VCF
   input/
param name=expression type=text label=javascript
   expression/
/inputs
  outputs
data format=vcf name=output/
/outputs
  stdio
exit_code range=1:/
exit_code range=:-1/
  /stdio
  help/help
   /tool



I still get an error:

(...)

   :24,289 (31) command is: java -cp 
$JVARKITDIR/commons-jexl-2.1.1.jar:$JVARKITDIR/commons-logging-1.1.1.jar:$JVARKITDIR/htsjdk-1.129.jar:$JVARKITDIR/snappy-java-1.0.3-rc3.jar:$JVARKITDIR/vcffilterjs.jar 
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e 
'variant!=nullX' -o 
/home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/files/000/dataset_27.dat 
/home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/files/000/dataset_1.dat; 
return_code=$?; c

(...)
galaxy.jobs DEBUG 2015-02-26 13:31:24,333 (31) Persisting job 
destination (destination id: local:///)
galaxy.jobs.runners.local DEBUG 2015-02-26 13:31:25,689 execution 
finished: 
/home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/job_working_directory/000/31/galaxy_31.sh
galaxy.jobs.output_checker INFO 2015-02-26 13:31:25,717 Job 31: Fatal 
error: Exit code 1 ()

galaxy.jobs DEBUG 2015-02-26 13:31:25,784 setting dataset state to ERROR

The error displayed in galaxy is just an empty VCF header (that why I 
asked about the error log)


Thank you for your help

PS: By the way, my argument was -e 'variant!=null;' , why do I see '-e 
'variant!=nullX'  in the log ?



Pierre


On Thu, Feb 26, 2015 at 10:59 AM, Pierre Lindenbaum
pierre.lindenb...@univ-nantes.fr wrote:

Hi Galaxy,

I'm trying to put one of my java tool in galaxy.

I've copied the required files in my tool directory under /tools/jvarkit (I
can see it galaxy)

 $ ls
 commons-jexl-2.1.1.jar
 commons-logging-1.1.1.jar
 htsjdk-1.129.jar
 snappy-java-1.0.3-rc3.jar
 vcffilterjs.jar
 vcffilterjs.xml



Here is the content of vcffilterjs.xml

   ?xml version=1.0?
   tool hidden=false
id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
version=1.0.0 name=vcffilterjs
 requirements
   requirement type=binaryjava/requirement
 /requirements
 command![CDATA[java -cp
$INSTALL_DIR/commons-jexl-2.1.1.jar:$INSTALL_DIR/commons-logging-1.1.1.jar:$INSTALL_DIR/htsjdk-1.129.jar:$INSTALL_DIR/snappy-java-1.0.3-rc3.jar:$INSTALL_DIR/vcffilterjs.jar
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e '${expression}'
-o ${output} ${input}   2 /tmp/error ]]/command
 inputs
   param format=vcf name=input type=data label=VCF input/
   param name=expression type=text label=javascript
expression/
 /inputs
 outputs
   data format=vcf name=output/
 /outputs
 stdio
   exit_code range=1:/
   exit_code range=:-1/
 /stdio
 help(...)/help
   /tool

When I run this tool, the log says:

NotFound: cannot find 'INSTALL_DIR'

If I replace $INSTALL_DIR with \$INSTALL_DIR ,

Yes, you need to escape the dollar sign.


the  error on stderr is :

 Error: Could not find or load main class
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS

How can I make this work ?

Try inserting something like this into the command as a diagnostic:

echo \$INSTALL_DIR amp;amp;

Where do you define $INSTALL_DIR? Is this environment variable
done at system level, or are you trying to do this within a Galaxy
defined package.

If the later, you need a requirements type=package ... tag,
which cross references a package defined within a
tool_dependencies.xml file. See for example:

https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod


Bonus question: is there a way to catch the error file to display it in

Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread John Chilton
Sorry I wasn't clear about that - it hasn't reached galaxy-dist yet -
you can download the latest snapshot of 15.03 release (I believe it is
running on usegalaxy.org as of yesterday) via this link instead
https://bitbucket.org/galaxy/galaxy-central/get/release_15.03.zip.

Also not need to escape $__tool_directory__  (so use
$__tool_directory__ instead of \$__tool_directory__).

-John

On Thu, Feb 26, 2015 at 9:40 AM, Pierre Lindenbaum
pierre.lindenb...@univ-nantes.fr wrote:
 On 02/26/2015 02:51 PM, John Chilton wrote:

 Just to make sure - since it hasn't been explicitly stated - is this
 tool being installed from the tool shed? The environment variable
 setup in tool_dependencies.xml will only be available for tool shed
 installs.


 no, my future plan is to put it in the tool shed but for now, I'm just
 trying to make it run in my local instance of galaxy.

 I'm sorry if that wasn't clear.


 I've just downloaded the latest version of galaxy via
 https://bitbucket.org/galaxy/galaxy-dist/get/tip.zip (
 galaxy-galaxy-dist-02ddea42faad.zip )
 and re-tried.


 I tried to print the variable $__tool_directory__ with the tool.xml below

 but it's not defined

 $ cat /tmp/error7.txt
 dir= .
 Error: Could not find or load main class
 com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS


 the xml:

?xml version=1.0?
tool hidden=false
id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
version=1.0.0 name=vcffilterjs
   requirements
 requirement type=binaryjava/requirement
   /requirements

   command![CDATA[echo dir=\$__tool_directory__ . 
/tmp/error7.txt  java -cp

 \$__tool_directory__/commons-jexl-2.1.1.jar:\$__tool_directory__/commons-logging-1.1.1.jar:\$__tool_directory__/htsjdk-1.129.jar:\$__tool_directory__/snappy-java-1.0.3-rc3.jar:\$__tool_directory__/vcffilterjs.jar
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e
'${expression}' -o ${output} ${input}  2 /tmp/error7.txt ]]/command
   inputs
 param format=vcf name=input type=data label=VCF
input/
 param name=expression type=text label=javascript
expression
 sanitizer
  valid initial=string.printable
  remove value=apos;/
 /valid
 /sanitizer
 /param

 /inputs
   outputs
 data format=vcf name=output/
 /outputs
   stdio
 exit_code range=1:/
 exit_code range=:-1/
   /stdio
   help/help
/tool


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Re: [galaxy-dev] custom java tools.xml : problem with classpath

2015-02-26 Thread Peter Cock
On Thu, Feb 26, 2015 at 12:38 PM, Pierre Lindenbaum
pierre.lindenb...@univ-nantes.fr wrote:
 Hi Peter,


 i wrote the tool_dependencies.xml


?xml version=1.0?
tool_dependency
 package name=jvarkit version=1.0.0
 install version=1.0.0
 actions
 action type=set_environment
 environment_variable name=JVARKITDIR
action=set_to$INSTALL_DIR/environment_variable
 /action
 /actions
 /install
 readme/readme
 /package
/tool_dependency




 and updated vcffilterjs.xml


?xml version=1.0?
tool hidden=false
id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
version=1.0.0 name=vcffilterjs
   requirements
   requirement type=package version=1.0.0jvarkit/requirement
 requirement type=binaryjava/requirement
   /requirements


   command![CDATA[java -cp

 \$JVARKITDIR/commons-jexl-2.1.1.jar:\$JVARKITDIR/commons-logging-1.1.1.jar:\$JVARKITDIR/htsjdk-1.129.jar:\$JVARKITDIR/snappy-java-1.0.3-rc3.jar:\$JVARKITDIR/vcffilterjs.jar
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e
'${expression}' -o ${output} ${input}  ]]/command
   inputs
 param format=vcf name=input type=data label=VCF
input/
 param name=expression type=text label=javascript
expression/
 /inputs
   outputs
 data format=vcf name=output/
 /outputs
   stdio
 exit_code range=1:/
 exit_code range=:-1/
   /stdio
   help/help
/tool



 I still get an error:

Could you confirm if the environment variable is being set now?

 (...)

:24,289 (31) command is: java -cp
 $JVARKITDIR/commons-jexl-2.1.1.jar:$JVARKITDIR/commons-logging-1.1.1.jar:$JVARKITDIR/htsjdk-1.129.jar:$JVARKITDIR/snappy-java-1.0.3-rc3.jar:$JVARKITDIR/vcffilterjs.jar
 com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e 'variant!=nullX'
 -o
 /home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/files/000/dataset_27.dat
 /home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/files/000/dataset_1.dat;
 return_code=$?; c
 (...)
 galaxy.jobs DEBUG 2015-02-26 13:31:24,333 (31) Persisting job destination
 (destination id: local:///)
 galaxy.jobs.runners.local DEBUG 2015-02-26 13:31:25,689 execution finished:
 /home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/job_working_directory/000/31/galaxy_31.sh
 galaxy.jobs.output_checker INFO 2015-02-26 13:31:25,717 Job 31: Fatal error:
 Exit code 1 ()
 galaxy.jobs DEBUG 2015-02-26 13:31:25,784 setting dataset state to ERROR

 The error displayed in galaxy is just an empty VCF header (that why I asked
 about the error log)

Did you check the stdout and stderr via the web interface?

 Thank you for your help

 PS: By the way, my argument was -e 'variant!=null;' , why do I see '-e
 'variant!=nullX'  in the log ?

You'll need to white list the semi-colon which Galaxy has replaced
as a security precaution (user free text can be exploited). See
sanitizer here:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

Peter
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