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1 <macros>
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2 <token name="@VERSION@">2.2.1</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="2.2.1">cufflinks</requirement>
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6 <yield />
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7 </requirements>
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8 </xml>
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9 <xml name="stdio">
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10 <stdio>
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11 <exit_code range="1:" />
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12 <exit_code range=":-1" />
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13 <regex match="Error:" />
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14 <regex match="Exception:" />
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15 </stdio>
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16 </xml>
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17 <xml name="condition_inputs">
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18 <!-- DEFAULT : use BAM/SAM files -->
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19 <conditional name="in_type">
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20 <param name="set_in_type" type="select" label="Input data type"
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21 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">
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22 <option value="BAM">SAM/BAM</option>
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23 <option value="CXB">Cuffquant (CXB)</option>
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24 <option value="CONDITION_LIST">List of single replicate conditions</option>
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25 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
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26 </param>
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27 <when value="BAM">
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28 <repeat name="conditions" title="Condition" min="2">
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29 <param name="name" title="Condition name" type="text" label="Name"/>
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30 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
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31 </repeat>
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32 </when>
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33 <when value="CXB">
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34 <repeat name="conditions" title="Condition" min="2">
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35 <param name="name" title="Condition name" type="text" label="Name"/>
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36 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
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37 </repeat>
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38 </when>
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39 <when value="CONDITION_LIST">
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40 <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" />
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41 </when>
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42 <when value="CONDITION_REPLICATE_LIST">
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43 <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" />
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44 </when>
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45 </conditional>
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46 </xml>
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47 <token name="@CONDITION_SAMPLES@">
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48 #if $in_type.set_in_type in ['BAM', 'CXB']
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49 #for $condition in $in_type.conditions:
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50 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
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51 $samples
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52 #end for
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53 #elif $in_type.set_in_type == 'CONDITION_LIST'
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54 #for $sample in $in_type.conditions:
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55 $sample
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56 #end for
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57 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
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58 #for $condition_list in $in_type.conditions:
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59 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
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60 $samples
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61 #end for
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62 #end if
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63 </token>
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64 <token name="@CONDITION_LABELS@">
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65 #import re
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66 #if $in_type.set_in_type in ['BAM', 'CXB']
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67 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\''
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68 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
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69 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\''
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70 #end if
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71 --labels $labels
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72 </token>
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73 <xml name="cufflinks_gtf_inputs">
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74 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
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75 <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)">
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76 <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" />
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77 </repeat>
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78 </xml>
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79 <token name="@CUFFLINKS_GTF_INPUTS@">
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80 ## Inputs.
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81 #for $input_file in $inputs:
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82 "${input_file}"
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83 #end for
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84 #for $additional_input in $additional_inputs:
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85 #for $input_file in $additional_input.additional_inputs:
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86 "${input_file}"
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87 #end for
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88 #end for
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89 </token>
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90 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
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91 </macros> |
