Hi Marine

In addition to Ross' comment earlier, there are a few points in the xml
I think they are wrong or at least I would code them differently - see
my comments in between your text below

On 05/30/2012 12:32 PM, Marine Rohmer wrote:
> Hi Hans,
>
> Here is my XML file in a simplificated version (no <conditionnal>
> parameters) , -i -r and -k are the mandatory arguments of my tool,
> written in C++:
>
>
> <tool id="myTool" name="myTool">
>
> <description> the description </description>
>
> <command interpreter="C++">
> /home/myName/work/galaxy-dist/tools/NGStools/myTool
> -i="${genome_index}"
> -r="${input}"
> -k="${kmer_length}"
> -o="${output_name}"
> </command>
>

There is no variable ${genome_index}, ${input},${output_name}. You
defined them as: "$i", "$r", and "$o" .

Hence, I would write:

    <command> /home/myName/work/galaxy-dist/tools/NGStools/myTool
      -i="$i"
      -r="$r"
      -k="$kmer_length"
      -o="$o"
    </command>cd

> <inputs>
> <param name="i" type="select" label="Genome index">
> <option value="Human"> path/to/Human </option>
> <option value="E.coli"> path/to/Escherichia coli </option>
> </param>
>
> <param format="txt" name="r" type="data" label="Source File"
> help="Select a file"/>
> <param format="raw" name="r" type="data" label="Source File"
> help="Select a file"/>
> <param format="doc" name="r" type="data" label="Source File"
> help="Select a file"/>
> <param format="fastq" name="r" type="data" label="Source File"
> help="Select a file"/>
>

I would write this in one line:

<param format="txt,raw,doc,fastq" name="r" type="data" label="Source
File" help="Select a file"/>

Also, have you defined the 'raw' and the 'doc' format?

> <param name="kmer_length" type="integer" min="15" max="150" value="21"
> label="k-mer length"/>
>
>
> <param name="o" type="text" optional="true" label="Output name"/>
>
>
> </inputs>
>
> <outputs>
> <data format="sam" name="myTool_outfile" label="myTool on
> ${database.value_label}" />
> </outputs>
>

How about:

<data format="sam" name="myTool_outfile" label="myTool on $o" />

> <tests>
> <test>
> </test>
> </tests>
>
> <help>
>
>
>
> </help>
>
> </tool>
> </tool>
>

there is one "</tool>" too much



Hope this helps, Hans


>
>
> Regards,
> Marine
>
>
>
> ------------------------------------------------------------------------
> *De :* Hans-Rudolf Hotz <hrh@fmi.ch>
> *À :* Marine Rohmer <marine.rohmer@yahoo.fr>
> *Cc :* "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
> *Envoyé le :* Mercredi 30 mai 2012 11h42
> *Objet :* Re: [galaxy-dev] Error executing tool: cannot find 'database'
>
> Hi Marine
>
> Could you please provide the tool definition xml file. Otherwise it is
> going to be difficult to guess, what is going wrong
>
> Regards, Hans
>
>
> On 05/30/2012 11:10 AM, Marine Rohmer wrote:
>  > Hi everyone,
>  >
>  > I'm trying with all my best to add an NGS tool into my local Galaxy
>  > instance.
>  > I've added my tool in tool_conf.xml, and made a XML file with all the
>  > <command>, <param> etc... I think it's pretty ok, and everything is
>  > correctly displayed on the Galaxy interface.
>  >
>  > However, when I execute my tool, Galaxy says to me :
>  >
>  > Error executing tool: cannot find 'database'
>  >
>  >
>  > And in my shell, I can see :
>  >
>  > 127.0.0.1 - - [30/May/2012:10:47:01 +0200] "GET
>  > /tool_runner?tool_id=myTool HTTP/1.1" 200 -
>  > "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux
>  > x86_64; rv:12.0) Gecko/20100101 Firefox/12.0"
>  > galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while
>  > attempting tool execution:
>  > Traceback (most recent call last):
>  > File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line
>  > 1345, in handle_input
>  > _, out_data = self.execute( trans, incoming=params, history=history )
>  > File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line
>  > 1661, in execute
>  > return self.tool_action.execute( self, trans, incoming=incoming,
>  > set_output_hid=set_output_hid, history=history, **kwargs )
>  > File
>  > "/home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py",
>  > line 333, in execute
>  > data.name = fill_template( output.label, context=params )
>  > File "/home/myName/work/galaxy-dist/lib/galaxy/util/template.py", line
>  > 9, in fill_template
>  > return str( Template( source=template_text, searchList=[context] ) )
>  > File
>  >
> "/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
>  > line 1004, in __str__
>  > return getattr(self, mainMethName)()
>  > File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
>  > NotFound: cannot find 'database'
>  > 127.0.0.1 - - [30/May/2012:10:47:07 +0200] "POST /tool_runner/index
>  > HTTP/1.1" 200 - "http://localhost:8080/tool_runner?tool_id=myTool"
>  > "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101
>  > Firefox/12.0"
>  >
>  > I'm a beginner in computer sciences, so I can't understand since over 1
>  > week what's happening ... Any idea what's wrong with this ?
>  > (I'm using Ubuntu LTS 12.04)
>  >
>  > All help will be very very appreciated !
>  >
>  > Thank you,
>  >
>  > Marine
>  >
>  >
>  > ___________________________________________________________
>  > 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/
>
>
>
> ------------------------------------------------------------------------
> *De :* Hans-Rudolf Hotz <hrh@fmi.ch>
> *À :* Marine Rohmer <marine.rohmer@yahoo.fr>
> *Cc :* "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
> *Envoyé le :* Mercredi 30 mai 2012 11h42
> *Objet :* Re: [galaxy-dev] Error executing tool: cannot find 'database'
>
> Hi Marine
>
> Could you please provide the tool definition xml file. Otherwise it is
> going to be difficult to guess, what is going wrong
>
> Regards, Hans
>
>
> On 05/30/2012 11:10 AM, Marine Rohmer wrote:
>  > Hi everyone,
>  >
>  > I'm trying with all my best to add an NGS tool into my local Galaxy
>  > instance.
>  > I've added my tool in tool_conf.xml, and made a XML file with all the
>  > <command>, <param> etc... I think it's pretty ok, and everything is
>  > correctly displayed on the Galaxy interface.
>  >
>  > However, when I execute my tool, Galaxy says to me :
>  >
>  > Error executing tool: cannot find 'database'
>  >
>  >
>  > And in my shell, I can see :
>  >
>  > 127.0.0.1 - - [30/May/2012:10:47:01 +0200] "GET
>  > /tool_runner?tool_id=myTool HTTP/1.1" 200 -
>  > "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux
>  > x86_64; rv:12.0) Gecko/20100101 Firefox/12.0"
>  > galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while
>  > attempting tool execution:
>  > Traceback (most recent call last):
>  > File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line
>  > 1345, in handle_input
>  > _, out_data = self.execute( trans, incoming=params, history=history )
>  > File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line
>  > 1661, in execute
>  > return self.tool_action.execute( self, trans, incoming=incoming,
>  > set_output_hid=set_output_hid, history=history, **kwargs )
>  > File
>  > "/home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py",
>  > line 333, in execute
>  > data.name = fill_template( output.label, context=params )
>  > File "/home/myName/work/galaxy-dist/lib/galaxy/util/template.py", line
>  > 9, in fill_template
>  > return str( Template( source=template_text, searchList=[context] ) )
>  > File
>  >
> "/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
>  > line 1004, in __str__
>  > return getattr(self, mainMethName)()
>  > File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
>  > NotFound: cannot find 'database'
>  > 127.0.0.1 - - [30/May/2012:10:47:07 +0200] "POST /tool_runner/index
>  > HTTP/1.1" 200 - "http://localhost:8080/tool_runner?tool_id=myTool"
>  > "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101
>  > Firefox/12.0"
>  >
>  > I'm a beginner in computer sciences, so I can't understand since over 1
>  > week what's happening ... Any idea what's wrong with this ?
>  > (I'm using Ubuntu LTS 12.04)
>  >
>  > All help will be very very appreciated !
>  >
>  > Thank you,
>  >
>  > Marine
>  >
>  >
>  > ___________________________________________________________
>  > 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/
>
>