New subject: FW: Tool Testing: field inputs that occur inside repeat tag

27 Feb 2015


      Helop aI've been testing (using planemo) some tools scheduled for toolshed publication.  My first test works, but Galaxy reports that the second one fails with:
"Parameter %s requires a value, but has no legal values defined" % self.name
AssertionError: Parameter filter_column requires a value, but has no legal values defined
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 500 None
I presume its because of extra stuff needed to name variables have to be referred-to when they are inside a repeat section?  Or is it just something pecular to do with data_table_sources?
<test><!-- Equivalent to output of old bccdc BLASTn XML to Tabular -->
    	<param name="blastxml_file" value="blast_reporting_1.blastxml"/>
    	<output name="tabular_file" file="blast_reporting_1a.tabular"/>
    	<param name="out_format" value="std"/>
    	<param name="column_labels" value="" />
    	<param name="drop_redundant_hits" value="true"/>
    				
    </test>
    <test>
    	<param name="blastxml_file" value="blast_reporting_1.blastxml"/>
    	<output name="tabular_file" file="blast_reporting_1b.tabular"/>
    	<param name="out_format" value="std"/>
    	<param name="column_labels" value="" />
    	<param name="drop_redundant_hits" value="true"/>
    	
    	<param name="filter_column" value="pident"/>
    	<param name="filter_comparison" value="gte"/>
    	<param name="filter_value" value="97"/>
    	
    </test>
The form repeat area:
<repeat name="filter_num" title="Numeric Filter" min="0" max="4">
<param name="filter_column" type="select" label="Col">
    		<options from_data_table="blast_reporting_fields">
    			<filter type="static_value" value="numeric" column="type" />
    			<filter type="sort_by" column="name"/>
    		</options>
    	</param>
    		
    	<repeat name="constraint" title="Constraint" min="1" max="3">
    		<param name="filter_comparison" type="select" label="Comparison">
    			<option value="gte">&gt;= </option>
    			<option value="gt">&gt;</option>
    			<option value="lt">&lt; </option>
    			<option value="lte">&lt;= </option>
    			<option value="==">equal to </option>
    			<option value="!=">not equal to </option>
    		</param>
    		
    		<param name="filter_value" type="text" value="" label="Value">
    			<validator type="regex" message="Please input a number">([0-9]+|[0-9]*.[0-9]+)</validator>
    		</param>
    		
    	</repeat>
    </repeat>
The working command section that sends the filter field info is:
#for $i, $my_repeat in enumerate( $filter_num ) 
    	$my_repeat.filter_column:
    	#for $i, $my_repeat2 in enumerate( $my_repeat.constraint ) 
    		$my_repeat2.filter_comparison $my_repeat2.filter_value,
    	#end for
    	;
    #end for
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada