Syntax issue for adding new tool

6 Feb 2012

      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'

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

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

Jeffrey Long

Louise-Amélie Schmitt

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