Changeset 1463:66be239241bc

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Timestamp:
08/01/08 14:34:16 (5 months ago)
Author:
greg
branch:
default
Message:

Fix for gops metadata param parser when strand column not included in input dataset, added new test for gops intersect. Fix for datatype converters - now use new approach to metadata params.

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  • lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml

    r1375 r1463  
    11<tool id="CONVERTER_fastqsolexa_to_qual_0" name="Convert Fastqsolexa to Qual"> 
    2   <command interpreter="python">fastqsolexa_to_qual_converter.py $input1 $output1 $input1.extension</command> 
     2  <command interpreter="python">fastqsolexa_to_qual_converter.py $input1 $output1 ${input1.extension}</command> 
    33  <inputs> 
    44    <param format="fastqsolexa" name="input1" type="data" label="Choose Fastqsolexa file"/> 

  • lib/galaxy/datatypes/converters/interval_to_bed_converter.xml

    r1129 r1463  
    22  <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> 
    33  <!-- Used on the metadata edit page. --> 
    4   <command interpreter="python">interval_to_bed_converter.py $output1 $input1 $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol</command> 
     4  <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command> 
    55  <inputs> 
    66    <page> 

  • lib/galaxy/datatypes/converters/maf_to_interval_converter.xml

    r1129 r1463  
    11<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals"> 
    22<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> 
    3   <command interpreter="python">maf_to_interval_converter.py $output1 $input1 $input1_dbkey</command> 
     3  <command interpreter="python">maf_to_interval_converter.py $output1 $input1 ${input1.metadata.dbkey}</command> 
    44  <inputs> 
    55    <page> 

  • lib/galaxy/tools/util/galaxyops/__init__.py

    r1323 r1463  
    1414    sys.exit( 1 ) 
    1515 
    16 # Default chrom, start, end, stran cols for a bed file 
     16# Default chrom, start, end, strand cols for a bed file 
    1717BED_DEFAULT_COLS = 0, 1, 2, 5 
    1818 
    …… 
    2020    """Parse a columns command line argument into a four-tuple""" 
    2121    if cols: 
    22         return map( lambda x: int( x ) - 1, cols.split(",") ) 
     22        col_list = map( lambda x: int( x ) - 1, cols.split(",") ) 
     23        if len( col_list ) == 3: 
     24            # We only have  chrom, start and end cols, so we need to add a strand col 
     25            col_list.append( -1 ) 
     26        return col_list 
    2327    else: 
    2428        return BED_DEFAULT_COLS 

  • tools/new_operations/intersect.xml

    r1451 r1463  
    5151      <output name="output" file="gops_intersect_bigint_out.interval" />      
    5252    </test> 
     53    <test> 
     54      <param name="input1" value="12.bed" ftype="bed" /> 
     55      <param name="input2" value="1.bed" ftype="bed" /> 
     56      <param name="min" value="1" /> 
     57      <param name="returntype" value="" /> 
     58      <output name="output" file="gops_intersect_no_strand_out.bed" />      
     59    </test> 
    5360  </tests> 
    5461  <help>