comparison cuff_macros.xml @ 2:b2ee2bef1926 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f

1:986b63735a5e

<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" />

            <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

    </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>

2:b2ee2bef1926

<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" />

            <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" label="Condition name" type="text"/>
                <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" label="Condition name" type="text"/>
                <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
            </repeat>
        </when>
        <when value="CONDITION_LIST">
            <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
        </when>
        <when value="CONDITION_REPLICATE_LIST">
            <param name="conditions" label="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

    </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>