Mercurial > repos > devteam > cuffmerge

annotate cuff_macros.xml @ 5:8cedf303be28 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
author iuc
date Fri, 20 Aug 2021 16:39:54 +0000
parents 7a9ca385b471
children f4bc1b2fc4d4
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0
e556721b9872 Uploaded
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1 <macros>
5
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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2 <token name="@VERSION@">2.2.1</token>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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3
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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4 <xml name="requirements">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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5 <requirements>
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6 <requirement type="package" version="2.2.1">cufflinks</requirement>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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7 <yield />
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8 </requirements>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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9 </xml>
2
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10
5
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11 <xml name="conditions_repeat" token_format="">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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12 <repeat name="conditions" title="Condition" min="2">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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13 <param name="name" label="Condition name" type="text">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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14 <validator type="empty_field" message="You must provide a condition name" />
8cedf303be28 "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="expression" message="Commas are not allowed in condition names">value and "," not in value</validator>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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16 </param>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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17 <param name="samples" label="Replicates" type="data" format="@FORMAT@" multiple="true"/>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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18 </repeat>
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19 </xml>
2
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20
5
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21 <xml name="condition_inputs">
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22 <!-- DEFAULT : use BAM/SAM files -->
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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23 <conditional name="in_type">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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24 <param name="set_in_type" type="select" label="Input data type"
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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25 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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26 <option value="BAM">SAM/BAM</option>
8cedf303be28 "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="CXB">Cuffquant (CXB)</option>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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28 <option value="CONDITION_LIST">List of single replicate conditions</option>
8cedf303be28 "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_REPLICATE_LIST">List of multiple replicate conditions</option>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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30 </param>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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31 <when value="BAM">
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32 <expand macro="conditions_repeat" format="sam,bam" />
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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33 </when>
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34 <when value="CXB">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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35 <expand macro="conditions_repeat" format="cxb" />
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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36 </when>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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37 <when value="CONDITION_LIST">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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38 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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39 </when>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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40 <when value="CONDITION_REPLICATE_LIST">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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41 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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42 </when>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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43 </conditional>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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44 </xml>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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45 <token name="@CONDITION_SAMPLES@"><![CDATA[
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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46 #if $in_type.set_in_type in ['BAM', 'CXB']
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47 #for $condition in $in_type.conditions:
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48 #set samples = ','.join([str($sample) for $sample in $condition.samples])
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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49 '$samples'
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50 #end for
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51 #elif $in_type.set_in_type == 'CONDITION_LIST'
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52 #for $sample in $in_type.conditions:
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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53 '$sample'
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54 #end for
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55 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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56 #for $condition_list in $in_type.conditions:
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57 #set samples = ','.join([str($sample) for $sample in $condition_list])
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58 '$samples'
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59 #end for
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60 #end if
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61 ]]></token>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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62 <token name="@CONDITION_LABELS@"><![CDATA[
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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63 #import re
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64 #if $in_type.set_in_type in ['BAM', 'CXB']
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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65 #set labels = "','".join([str($condition.name) for $condition in $in_type.conditions])
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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66 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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67 #set labels = "','".join([str($condition).replace(',', '_') for $condition in $in_type.conditions.keys()])
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68 #end if
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69 --labels '$labels'
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70 ]]></token>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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71 <xml name="cufflinks_gtf_inputs">
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72 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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73 </xml>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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74 <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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75 ## Inputs.
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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76 #for $i, $input_file in enumerate($inputs):
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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77 ln -s '${input_file}' input_$i &&
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78 #end for
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79 ]]></token>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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80 <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[
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81 ## Inputs.
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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82 #for $i, $input_file in enumerate($inputs):
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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83 'input_$i'
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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84 #end for
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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85 ]]></token>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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86 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
4
7a9ca385b471 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
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87
5
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88 <xml name="citations">
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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89 <citations>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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90 <citation type="doi">10.1038/nbt.1621</citation>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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91 <yield/>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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92 </citations>
8cedf303be28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
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93 </xml>
4
7a9ca385b471 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
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94
1
02f427c3614b planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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95 </macros>