<macros>
  <token name="@VERSION@">2.2.1</token>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="2.2.1">cufflinks</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="stdio">
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
  </xml>
  <xml name="condition_inputs">
    <!-- DEFAULT : use BAM/SAM files -->
    <conditional name="in_type">
        <param name="set_in_type" type="select" label="Input data type"
            help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">
            <option value="BAM">SAM/BAM</option>
            <option value="CXB">Cuffquant (CXB)</option>
            <option value="CONDITION_LIST">List of single replicate conditions</option>
            <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
        </param>
        <when value="BAM">
            <repeat name="conditions" title="Condition" min="2">
                <param name="name" title="Condition name" type="text" label="Name"/>
                <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
            </repeat>
        </when>
        <when value="CXB">
            <repeat name="conditions" title="Condition" min="2">
                <param name="name" title="Condition name" type="text" label="Name"/>
                <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
            </repeat>
        </when>
        <when value="CONDITION_LIST">
            <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" />
        </when>
        <when value="CONDITION_REPLICATE_LIST">
            <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" />
        </when>
    </conditional>
  </xml>
  <token name="@CONDITION_SAMPLES@">
            #if $in_type.set_in_type in ['BAM', 'CXB']
                #for $condition in $in_type.conditions:
                    #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
                    $samples
                #end for
            #elif $in_type.set_in_type == 'CONDITION_LIST'
                #for $sample in $in_type.conditions:
                    $sample
                #end for
            #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
                #for $condition_list in $in_type.conditions:
                    #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
                    $samples
                #end for
            #end if
  </token>
  <token name="@CONDITION_LABELS@">
            #import re
            #if $in_type.set_in_type in ['BAM', 'CXB']
                #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\''
            #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
                #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\''
            #end if
            --labels $labels
  </token>
  <xml name="cufflinks_gtf_inputs">
    <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
    <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)">
      <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" />
    </repeat>
  </xml>
  <token name="@CUFFLINKS_GTF_INPUTS@">
            ## Inputs.
            #for $input_file in $inputs:
                "${input_file}"
            #end for
            #for $additional_input in $additional_inputs:
                #for $input_file in $additional_input.additional_inputs:
                  "${input_file}"
                #end for
            #end for
  </token>
  <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
</macros>