[galaxy-dev] tool with conditional parameter broken on release 2014.08.11

5 Dec 2014

      Dear,

I am looking for help after updating our Galaxy production server to release 2014.08.11, one of our in-house tool does not load in Galaxy anymore. I do think the problem is related to the conditional parameter because when I comment this section out Galaxy does display it. Any ideas where the problem could be?

Here is the xml file:

<tool id="hm" name="heatmap-public">
  <description>Creates a heatmap from public datasets</description>

  <command interpreter="R --vanilla --slave -f">
    #silent sys.stderr.write("!!!! Cheetah Template Variables !!!!\n")
    #for k,v in $searchList[2].items()
    #silent   sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))
    #end for

    ## path to the dataset selected extracted from the 'cri_datasets' data table (tool-data/cri/datasets.loc)
    #import os
    #set $dataset_relative_path = filter( lambda x: str( x[0] ) == str( $dataset.name ), $__app__.tool_data_tables[ 'cri_datasets' ].get_fields() )[0][-1]
    #set $dataset_path = os.path.join($__tool_data_path__, $dataset_relative_path)

    hm.R --args 
      $dataset.name
      $dataset_path 
      $input 
      $col 
      $output_html 
       #if not $varExists('$output_pdf')
        none
      #else
        $output_pdf
      #end if
      $output_html.files_path 
      $dataset.list
      $gene 
      $dataset.label 
      $dataset.sample
      ## optional arguments set to 'none' when not relevant to a particular dataset
      #if not $varExists('$dataset.blocks')
        none
      #else
        $dataset.blocks
      #end if
      #if not $varExists('$dataset.group')
        none
      #else
        $dataset.group
      #end if
      $scaling
      $coloring.coloring
      ## optional arguments set to '0' when not relevant to a colour option
      #if not $varExists('$coloring.limit')
        0
      #else
        $coloring.limit
      #end if
      $cexrow
      $cexcol

      2>stderr || cat stderr 1>&2
  </command>

  <inputs>
    <param name="input" type="data" format="tabular,txt" label="Gene List" help="Tab delimited text file containing a list of gene symbols"/>
    <param name="col" type="data_column" data_ref="input" numerical="False" label="Column" help="Column containing gene symbols (only available for tabular input file)" />

      <conditional name="dataset">
        <param name="name" type="select" label="Dataset name">
          <options from_data_table="cri_datasets">
            <column name="name" index="1"/>
            <column name="value" index="0"/>
            <filter type="multiple_splitter" column="4" separator="," />
            <filter type="static_value" value="heatmap" column="4" />
          </options>
        </param>

        <when value="glinsky">
          <param name="list" type="select" label="Input type" help="Type of input (Genes or Affymetrix probe IDs)">
            <option value="genes" selected="true">Genes</option>
            <option value="probes">Probes</option>
          </param>
          <param name="sample" type="select" label="Sample ordering" help="Cluster samples or order samples by Recurrence, Pathological Gleason grade or Surgical margin status">
            <option value="cluster" selected="true">Cluster</option>
            <option value="recurrence">Recurrence</option>
            <option value="gleason">Gleason grade</option>
            <option value="sms">Surgical margin status</option>
          </param> 
          <param name="blocks" type="select" label="Add coloured blocks" help="Add coloured blocks for Recurrence, Pathological Gleason grade, Surgical margin status (Negative/Positive), all three or none">
            <option value="recurrence" selected="true">Recurrence</option>
            <option value="gleason">Gleason grade</option>
            <option value="sms">Surgical margin status</option>
            <option value="all">All three</option>
            <option value="none">No blocks</option>
          </param>
          <param name="label" type="select" label="Gene labels" help="Label rows of heatmap with Probe IDs, Gene symbols or both">
            <option value="both" selected="true">Both</option>
            <option value="gene">Gene</option>
            <option value="probe">Probe</option>
          </param>
        </when>

        <when value="varambally">
          <param name="list" type="select" label="Input type" help="Type of input (Genes or Affymetrix probe IDs)">
            <option value="genes" selected="true">Genes</option>
            <option value="probes">Probes</option>
          </param>
          <param name="sample" type="select" label="Sample ordering" help="Cluster samples or order by Group">
            <option value="cluster" selected="true">Cluster</option>
            <option value="group">Group</option>
          </param>
          <param name="label" type="select" label="Gene labels" help="Label rows of heatmap with Affymetrix Probe IDs, Gene symbols or both">
            <option value="both" selected="true">Both</option>
            <option value="gene">Gene</option>
            <option value="probe">Probe</option>
          </param>
        </when>

        <when value="taylor">
          <param name="list" type="select" label="Input type" help="Type of input (Genes or Refseq Accession number)">
            <option value="genes" selected="true">Genes</option>
            <option value="access">Accession number</option>
          </param>
          <param name="sample" type="select" label="Sample ordering" help="Cluster samples or order samples by Recurrence, Gleason Grade, Surgical Margin Status, Group or Pairs (when matched pairs selected)">
            <option value="cluster" selected="true">Cluster</option>
            <option value="recurrence">Recurrence</option>
            <option value="gleason">Gleason grade</option>
            <option value="sms">Surgical margin status</option>
            <option value="group">Group</option>
            <option value="pairs">Pairs</option>
          </param>
          <param name="blocks" type="select" label="Add coloured blocks" help="Add coloured blocks for Recurrence (N/Y), Pathological Gleason grade (Low/High), Surgical margin status (Negative/Positive), Group (Benign/Primary/Met/Cell line), All four or None">
            <option value="recurrence" selected="true">Recurrence</option>
            <option value="gleason">Gleason grade</option>
            <option value="sms">Surgical margin status</option>
            <option value="group">Group</option>
            <option value="all">All four</option>
            <option value="none">No blocks</option>
          </param>
	  <param name="group" type="select" label="Select groups" help="Select groups included in the plot, All, No cell line, Matched benign primary pairs, Cancer samples (Primary and Metastatic samples)">
	    <option value="all" selected="true">All</option>
            <option value="nocellline">No cell line</option>
            <option value="pairs">Matched pairs</option>
            <option value="cancer">Cancer Samples</option>
          </param>            
          <param name="label" type="select" label="Gene labels" help="Label rows of heatmap with Refseq Accession number, Gene symbols or both">
            <option value="both" selected="true">Both</option>
            <option value="gene">Gene</option>
            <option value="access">Accession number</option>
          </param>
        </when>
      </conditional>

    <param name="gene" type="select" label="Gene clustering" help="Cluster genes or to retain original ordering">
      <option value="no" selected="true">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="scaling" type="select" label="Heatmap scaling" help="Chose how probes are scaled, median scaled (minus median), robust z-score (minus median divide median absolute deviation), or z-score (minus mean divide standard deviation">
      <option value="median" selected="true">Median scaled</option>
      <option value="robustz">Robust z-score</option>
      <option value="zscore">Z-score</option>
    </param>

      <conditional name="coloring">      
        <param name="coloring" type="select" label="Heatmap colouring" help="How colouring is chosen, by heatmap i.e. colouring is specific for heatmap, or fixed i.e. the same probes in different heatmaps will have the same colour">
          <option value="heatmap" selected="true">Heatmap</option>
          <option value="fixed">Fixed</option>
        </param>
          <when value="fixed">
            <param name="limit" type="float" value="3" label="Fixed limits" help="When chosing the fixed colour option, this value is the limit for choosing colours" />     
         </when>
      </conditional>
    <param name="cexrow" type="float" label="Scale for Gene (row) Labels" min="0" value="0.9" help="1 is normal, use a lower value if the gene names are overlapping, a higher value if they are too small" />
    <param name="cexcol" type="float" label="Scale for Sample (column) Labels" min="0" value="1.0" help="1 is normal, use a lower value if the sample names are overlapping, a higher value if they are too small" /> 
    <param name="pdf" type="boolean" label="PDF output" help="Tick if PDF output is required in addition to html output" />

  </inputs>

  <outputs>
    <data format="html" name="output_html" />
    <data format="pdf" name="output_pdf">
      <filter>pdf is True</filter>
    </data>
  </outputs>

</tool>

Here is the error message:
Error - <type 'exceptions.ValueError'>: ('No case matched value:', 'dataset', None)
URL: http://uk-cri-lbio06/galaxy/tool_runner?tool_id=hm
File '/opt/local/home/webapp/galaxy/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/opt/local/home/webapp/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/opt/local/home/webapp/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '/opt/local/home/webapp/galaxy/lib/galaxy/web/framework/base.py', line 132 in __call__
  return self.handle_request( environ, start_response )
File '/opt/local/home/webapp/galaxy/lib/galaxy/web/framework/base.py', line 190 in handle_request
  body = method( trans, **kwargs )
File '/opt/local/home/webapp/galaxy/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', line 90 in index
  template, vars = tool.handle_input( trans, params.__dict__ )
File '/opt/local/home/webapp/galaxy/lib/galaxy/tools/__init__.py', line 2116 in handle_input
  state, state_new = self.__fetch_state( trans, expanded_incoming, history, all_pages=all_pages )
File '/opt/local/home/webapp/galaxy/lib/galaxy/tools/__init__.py', line 2230 in __fetch_state
  state = self.new_state( trans, history=history, all_pages=all_pages )
File '/opt/local/home/webapp/galaxy/lib/galaxy/tools/__init__.py', line 2015 in new_state
  self.fill_in_new_state( trans, inputs, state.inputs, history=history )
File '/opt/local/home/webapp/galaxy/lib/galaxy/tools/__init__.py', line 2024 in fill_in_new_state
  state[ input.name ] = input.get_initial_value( trans, context, history=history )
File '/opt/local/home/webapp/galaxy/lib/galaxy/tools/parameters/grouping.py', line 527 in get_initial_value
  current_case = self.get_current_case( test_value, trans )
File '/opt/local/home/webapp/galaxy/lib/galaxy/tools/parameters/grouping.py', line 480 in get_current_case
  raise ValueError( "No case matched value:", self.name, str_value )
ValueError: ('No case matched value:', 'dataset', None)

Many thanks.
Kind regards,
Anne.
--
Dr Anne Pajon - Bioinformatics Core
Cancer Research UK - Cambridge Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631