comparison cuffdiff_wrapper.xml @ 7:b5562b9a55c7

Use same bias_correction cached param as devteam cuffdiff

6:137aab1d9ac1

                #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

                <conditional name="seq_source">
                  <param name="index_source" type="select" label="Reference sequence data">
                    <option value="cached">Locally cached</option>
                    <option value="history">History</option>
                  </param>
                  <when value="cached"></when>
                  <when value="history">
                      <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                  </when>
                </conditional>
            </when>

7:b5562b9a55c7

                #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__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')}
                #end if
            #end if

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

                <conditional name="seq_source">
                  <param name="index_source" type="select" label="Reference sequence data">
                    <option value="cached">Locally cached</option>
                    <option value="history">History</option>
                  </param>
                  <when value="cached">
                    <param name="index" type="select" label="Using reference genome">
                      <options from_data_table="fasta_indexes">
                        <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
                        <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
                      </options>
                    </param>
                  </when>
                  <when value="history">
                      <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                  </when>
                </conditional>
            </when>