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">>= </option> <option value="gt">></option> <option value="lt">< </option> <option value="lte"><= </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