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annotate cuff_macros.xml @ 15:43b36b3d4333 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author iuc
date Tue, 16 Jun 2020 13:00:02 -0400
parents d3ae7d9c2202
children af3e173cad7f
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1 <macros>
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2 <token name="@VERSION@">2.2.1</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="2.2.1">cufflinks</requirement>
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7 <yield />
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8 </requirements>
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9 </xml>
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11 <xml name="condition_inputs">
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12 <!-- DEFAULT : use BAM/SAM files -->
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13 <conditional name="in_type">
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14 <param name="set_in_type" type="select" label="Input data type"
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15 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">
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16 <option value="BAM">SAM/BAM</option>
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17 <option value="CXB">Cuffquant (CXB)</option>
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18 <option value="CONDITION_LIST">List of single replicate conditions</option>
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19 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
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20 </param>
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21 <when value="BAM">
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22 <repeat name="conditions" title="Condition" min="2">
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23 <param name="name" label="Condition name" type="text"/>
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24 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
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25 </repeat>
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26 </when>
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27 <when value="CXB">
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28 <repeat name="conditions" title="Condition" min="2">
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29 <param name="name" label="Condition name" type="text"/>
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30 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
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31 </repeat>
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32 </when>
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33 <when value="CONDITION_LIST">
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34 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
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35 </when>
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36 <when value="CONDITION_REPLICATE_LIST">
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37 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
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38 </when>
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39 </conditional>
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40 </xml>
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41 <token name="@CONDITION_SAMPLES@">
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42 #if $in_type.set_in_type in ['BAM', 'CXB']
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43 #for $condition in $in_type.conditions:
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44 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
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45 '$samples'
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46 #end for
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47 #elif $in_type.set_in_type == 'CONDITION_LIST'
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48 #for $sample in $in_type.conditions:
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49 '$sample'
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50 #end for
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51 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
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52 #for $condition_list in $in_type.conditions:
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53 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
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54 '$samples'
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55 #end for
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56 #end if
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57 </token>
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58 <token name="@CONDITION_LABELS@">
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59 #import re
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60 #if $in_type.set_in_type in ['BAM', 'CXB']
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61 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\''
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62 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
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63 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\''
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64 #end if
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65 --labels $labels
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66 </token>
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67 <xml name="cufflinks_gtf_inputs">
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68 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
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69 </xml>
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43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
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70 <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[
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71 ## Inputs.
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72 #for $i, $input_file in enumerate($inputs):
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73 ln -s '${input_file}' input_$i &&
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74 #end for
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75 ]]></token>
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76 <token name="@CUFFLINKS_GTF_INPUTS@">
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77 ## Inputs.
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78 #for $i, $input_file in enumerate($inputs):
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79 'input_$i'
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80 #end for
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81 </token>
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82 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
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84 <xml name="citations">
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85 <citations>
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86 <citation type="doi">10.1038/nbt.1621</citation>
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87 <yield/>
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88 </citations>
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89 </xml>
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90
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91 </macros>