comparison cuffdiff_wrapper.xml @ 1:60a52f8460a1

Fix bias correction.

0:0dabb2ed6eb1

            -u
            #end if

            ## Bias correction?
            #if $bias_correction.do_bias_correction == "Yes":
	        -b
                #if $bias_correction.seq_source.index_source == "history":
                    --ref_file=$bias_correction.seq_source.ref_file
                #else:
                    --ref_file="None"
                #end if
                --dbkey=${gtf_input.metadata.dbkey} 
                --index_dir=${GALAXY_DATA_INDEX_DIR}
            #end if

            #set labels = ','.join( [ str( $condition.name ) for $condition in $conditions ] )
            --labels $labels

            </when>
        </conditional>
    </inputs>

    <stdio>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <outputs>
        <!-- Optional read group datasets. -->

1:60a52f8460a1

            -u
            #end if

            ## Bias correction?
            #if $bias_correction.do_bias_correction == "Yes":
               -b
                #if $bias_correction.seq_source.index_source == "history":
                    ## Custom genome from history.
                    $bias_correction.seq_source.ref_file
                #else:
                    ## Built-in genome.
                    ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
                #end if
            #end if

            #set labels = ','.join( [ str( $condition.name ) for $condition in $conditions ] )
            --labels $labels

            </when>
        </conditional>
    </inputs>

    <stdio>
        <regex match="Error" source="both" level="fatal" description="Error"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <outputs>
        <!-- Optional read group datasets. -->