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annotate cuff_macros.xml @ 17:04adc9db1581 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 52b81aad3194e02a04ec09eea1aa0c1e9301e942
author iuc
date Wed, 23 Oct 2024 22:12:19 +0000
parents 22cf48ad7b16
children
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b6e3849293b1 Uploaded
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1 <macros>
16
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2 <token name="@TOOL_VERSION@">2.2.1</token>
22cf48ad7b16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 80b06e80066b32ad53ed418628992f056444256f
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3 <token name="@PROFILE@">23.1</token>
15
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4
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">cufflinks</requirement>
15
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8 <yield />
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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9 </requirements>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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10 </xml>
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11
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12 <xml name="conditions_repeat" token_format="">
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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13 <repeat name="conditions" title="Condition" min="2">
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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14 <param name="name" label="Condition name" type="text">
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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15 <validator type="empty_field" message="You must provide a condition name" />
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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16 <validator type="expression" message="Commas are not allowed in condition names">value and "," not in value</validator>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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17 </param>
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18 <param name="samples" label="Replicates" type="data" format="@FORMAT@" multiple="true"/>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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19 </repeat>
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20 </xml>
12
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21
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22 <xml name="condition_inputs">
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23 <!-- DEFAULT : use BAM/SAM files -->
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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24 <conditional name="in_type">
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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25 <param name="set_in_type" type="select" label="Input data type"
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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26 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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27 <option value="BAM">SAM/BAM</option>
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28 <option value="CXB">Cuffquant (CXB)</option>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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29 <option value="CONDITION_LIST">List of single replicate conditions</option>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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30 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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31 </param>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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32 <when value="BAM">
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33 <expand macro="conditions_repeat" format="sam,bam" />
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34 </when>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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35 <when value="CXB">
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36 <expand macro="conditions_repeat" format="cxb" />
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37 </when>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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38 <when value="CONDITION_LIST">
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39 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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40 </when>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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41 <when value="CONDITION_REPLICATE_LIST">
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42 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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43 </when>
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44 </conditional>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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45 </xml>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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46 <token name="@CONDITION_SAMPLES@"><![CDATA[
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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47 #if $in_type.set_in_type in ['BAM', 'CXB']
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48 #for $condition in $in_type.conditions:
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49 #set samples = ','.join([str($sample) for $sample in $condition.samples])
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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50 '$samples'
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51 #end for
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52 #elif $in_type.set_in_type == 'CONDITION_LIST'
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53 #for $sample in $in_type.conditions:
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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54 '$sample'
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55 #end for
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56 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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57 #for $condition_list in $in_type.conditions:
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58 #set samples = ','.join([str($sample) for $sample in $condition_list])
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59 '$samples'
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60 #end for
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61 #end if
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62 ]]></token>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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63 <token name="@CONDITION_LABELS@"><![CDATA[
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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64 #import re
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65 #if $in_type.set_in_type in ['BAM', 'CXB']
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66 #set labels = "','".join([str($condition.name) for $condition in $in_type.conditions])
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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67 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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68 #set labels = "','".join([str($condition).replace(',', '_') for $condition in $in_type.conditions.keys()])
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69 #end if
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70 --labels '$labels'
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71 ]]></token>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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72 <xml name="cufflinks_gtf_inputs">
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73 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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74 </xml>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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75 <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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76 ## Inputs.
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77 #for $i, $input_file in enumerate($inputs):
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78 ln -s '${input_file}' input_$i &&
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79 #end for
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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80 ]]></token>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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81 <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[
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04adc9db1581 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 52b81aad3194e02a04ec09eea1aa0c1e9301e942
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82 ## Inputs.
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86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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83 #for $i, $input_file in enumerate($inputs):
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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84 'input_$i'
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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85 #end for
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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86 ]]></token>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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87 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
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6a6717a5f421 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
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88
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86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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89 <xml name="citations">
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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90 <citations>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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91 <citation type="doi">10.1038/nbt.1621</citation>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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92 <yield/>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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93 </citations>
86285ddd4512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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94 </xml>
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6a6717a5f421 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
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95
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8160c8ea4eb9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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96 </macros>