Hi all,

I am having trouble with what looked to me at first to be a "simple" syntactical issue with writing the XML wrapper for a new Galaxy tool.  I had thought this would be easy, but perhaps I am missing something incredibly simple, as I am having no success at all.  The relevant parts look something like this:  

<command interpreter="sh">

  mycommand.sh

        -i $input

  #if $param_file.use_params == "true"#

  -p $params

  #end if

  </command>

  <inputs>

  <param format="fasta" name="input" type="data" label="Source File"/> 

  <conditional name="param_file">

  <param name="use_params" type="select" label="Use custom parameter file?">

  <option value="true">Yes</option>

  <option value="false" selected="true">No</option>

  </param>

  <when value="true">

  <param format="text" name="params" type="data" label="Parameter File" value=""/>

  </when>

  </conditional>

 

  </inputs>

It's very simple, I just want the line "-p $params" to appear in the command line when the parameter "use_params" parameter is set to true.  

However, when building the command line statement to run, I get this error: 

----------------------

Traceback (most recent call last):

  File "/Users/jrl909/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 59, in run_job

    job_wrapper.prepare()

  File "/Users/jrl909/Galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 424, in prepare

    self.command_line = self.tool.build_command_line( param_dict )

  File "/Users/jrl909/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1827, in build_command_line

    command_line = fill_template( self.command, context=param_dict )

  File "/Users/jrl909/Galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template

    return str( Template( source=template_text, searchList=[context] ) )

  File "/Users/jrl909/Galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__

    return getattr(self, mainMethName)()

  File "cheetah_DynamicallyCompiledCheetahTemplate_1328561167_73_97196.py", line 84, in respond

NotFound: cannot find 'use_params' while searching for 'param_file.use_params'

michael

-------------------

As far as I can tell, the syntax I've used here is the same as that found in the example file suggested by the Galaxy documentation: interval2maf.xml  (what I see as the "relevant" sections being reproduced below):

---------------

<command interpreter="python">

    #if $maf_source_type.maf_source == "user" #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species

    #else                                     #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species

    #end if# --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species

    #if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"#

        --remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns

    #end if

  </command>

  <inputs>

    ...

    blahblahblah

    ...

    <conditional name="split_blocks_by_species_selector">

      <param name="split_blocks_by_species" type="select" label="Split blocks by species" help="Not usually applicable. See help below for more information.">

        <option value="split_blocks_by_species">Split by species</option>

        <option value="dont_split_blocks_by_species" selected="true">Do not split</option>

      </param>

      <when value="dont_split_blocks_by_species">

        <!-- do nothing here -->

      </when>

      <when value="split_blocks_by_species">

        <param name="remove_all_gap_columns" type="select" label="Collapse empty alignment columns">

          <option value="remove_all_gap_columns" selected="true">Collapse empty columns</option>

          <option value="do_not_remove_all_gap_columns">Do not collapse</option>

        </param>

      </when>

    </conditional>

   </inputs>

-------------------

As you can see, the field 'split_blocks_by_species' is referenced in an #if-block in the command specification the same way my 'use_params' field is.  

I would like very much to know the apparently crucial difference that I'm missing!  

Thanks,

-Jeff

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