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annotate chipseeker.xml @ 4:4fbd735886dd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
author rnateam
date Tue, 04 Dec 2018 10:02:01 -0500
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children 3ff6333973aa
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4fbd735886dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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1 <tool id="chipseeker" name="ChIPseeker" version="1.16.2">
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2 <description>for ChIP peak annotation and visualization</description>
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3 <requirements>
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4 <requirement type="package" version="1.16.1">bioconductor-chipseeker</requirement>
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5 <requirement type="package" version="1.4.4">r-optparse</requirement>
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6 </requirements>
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7 <version_command><![CDATA[
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8 echo $(R --version | grep version | grep -v GNU)", ChIPseeker version" $(R --vanilla --slave -e "library(ChIPseeker); cat(sessionInfo()\$otherPkgs\$ChIPseeker\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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9 ]]></version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #set gtf = "refgtf"
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12 #if $gtf_source.gtf_source_select == "history":
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13 ln -s '${gtf_source.gtf_hist}' $gtf &&
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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14 #else if $gtf_source.gtf_source_select == "cached":
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15 ln -s '${gtf_source.gtf_builtin.fields.path}' $gtf &&
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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16 #end if
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17
0
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18 #if $rscript:
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19 cp '$__tool_directory__/chipseeker.R' '$out_rscript' &&
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20 #end if
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22 Rscript '$__tool_directory__/chipseeker.R'
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23
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24 -i '$peaks'
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25 -G '$gtf'
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26 -u $adv.upstream
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27 -d $adv.downstream
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28 #if $adv.flankgeneinfo:
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29 -F $adv.flankgeneinfo
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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30 -D $adv.flankgenedist
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31 #end if
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32 -f $format
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33 #if $pdf:
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34 -p $pdf
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35 #end if
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36 -r $rdata
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37 ]]>
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38 </command>
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39 <inputs>
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40 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
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41 <conditional name="gtf_source">
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42 <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
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43 <option value="cached" selected="true">Use a built-in GTF</option>
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44 <option value="history">Use a GTF from history</option>
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45 </param>
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46 <when value="cached">
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47 <param name="gtf_builtin" type="select" label="Select a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">
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48 <options from_data_table="gene_sets">
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49 <filter type="sort_by" column="2" />
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50 <validator type="no_options" message="No GTF file is available." />
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51 </options>
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52 </param>
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53 </when>
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54 <when value="history">
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55 <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" />
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56 </when>
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57 </conditional>
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58 <param name="format" type="select" label="Output Format">
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59 <option value="interval" selected="True">Interval</option>
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60 <option value="tabular">Tabular (tab-separated)</option>
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61 </param>
1
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62 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />
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63 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
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64 <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"
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65 help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">
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66 </param>
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67
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68 <section name="adv" expanded="false" title="Advanced Options">
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69 <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." />
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70 <param name="downstream" type="integer" min="0" value="3000" label="TSS downstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb."/>
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71 <param name="flankgeneinfo" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Add flanking gene information?" help="If specified all genes within the flanking gene distance are reported for each peak. Default: No."/>
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72 <param name="flankgenedist" type="integer" min="0" value="5000" label="Flanking gene distance" help="If flanking gene info is turned on the flanking distance can be specified. Default: 5000."/>
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73 </section>
0
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74 </inputs>
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75
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76 <outputs>
1
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77 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >
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78 <change_format>
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79 <when input="format" value="tabular" format="tabular" />
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80 </change_format>
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81 </data>
0
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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82 <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots">
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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83 <filter>pdf</filter>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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84 </data>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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85 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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86 <filter>rscript</filter>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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87 </data>
2
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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parents: 1
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88 <data name="out_rdata" format="rdata" from_work_dir="ChIPseeker_analysis.RData" label="${tool.name} on ${on_string}: RData file">
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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89 <filter>rdata</filter>
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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90 </data>
0
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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91 </outputs>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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92
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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93 <tests>
1
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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94 <!-- Ensure bed and GTF inputs and all outputs work -->
2
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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parents: 1
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95 <test expect_num_outputs="4">
1
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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96 <param name="peaks" value="in.bed" ftype="bed"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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97 <param name="gtf_source_select" value="history"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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98 <param name="gtf_hist" value="in.gtf"/>
0
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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99 <param name="rscript" value="True"/>
2
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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100 <param name="rdata" value="True"/>
1
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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101 <output name="out_tab" ftype="interval" file="out.int" />
0
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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102 <output name="out_plots" file="out.pdf" compare="sim_size"/>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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103 <output name="out_rscript" >
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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104 <assert_contents>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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105 <has_text_matching expression="peakAnno.*annotatePeak" />
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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106 </assert_contents>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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107 </output>
2
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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parents: 1
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108 <output name="out_rdata" file="out.rdata" compare="sim_size" />
0
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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109 </test>
1
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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110 <!-- Ensure built-in GTF works -->
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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111 <test expect_num_outputs="2">
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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112 <param name="peaks" value="in.interval" ftype="interval"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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113 <param name="gtf_source_select" value="cached"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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114 <output name="out_tab" ftype="interval" file="outint.int" />
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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115 <output name="out_plots" file="out.pdf" compare="sim_size"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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116 </test>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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117 <!-- Ensure tabular output works -->
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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118 <test expect_num_outputs="2">
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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diff changeset
119 <param name="peaks" value="in.interval" ftype="interval"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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120 <param name="gtf_source_select" value="history"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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diff changeset
121 <param name="gtf_hist" value="in.gtf"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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diff changeset
122 <param name="format" value="tabular"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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diff changeset
123 <output name="out_tab" ftype="tabular" file="outint.tab" />
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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124 <output name="out_plots" file="out.pdf" compare="sim_size"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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diff changeset
125 </test>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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126 <!-- Ensure TSS region specification works -->
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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127 <test expect_num_outputs="2">
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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128 <param name="peaks" value="in.interval" ftype="interval"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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129 <param name="gtf_source_select" value="history"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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130 <param name="gtf_hist" value="in.gtf"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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131 <param name="upstream" value="1000" />
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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132 <param name="downstream" value="1000" />
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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133 <param name="format" value="tabular"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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134 <output name="out_tab" ftype="tabular" file="outtss.tab" />
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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135 <output name="out_plots" file="out.pdf" compare="sim_size"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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136 </test>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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137 <!-- Ensure flanking genes works -->
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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138 <test expect_num_outputs="2">
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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139 <param name="peaks" value="in.interval" ftype="interval"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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140 <param name="gtf_source_select" value="history"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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141 <param name="gtf_hist" value="in.gtf"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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142 <param name="flankgeneinfo" value="True" />
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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143 <param name="format" value="tabular"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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144 <output name="out_tab" ftype="tabular" file="outflank.tab" />
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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145 <output name="out_plots" file="out.pdf" compare="sim_size"/>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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146 </test>
4
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147 <!-- Ensure the tool works when no plots are outputed -->
4fbd735886dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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148 <test expect_num_outputs="1">
4fbd735886dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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149 <param name="peaks" value="in.interval" ftype="interval"/>
4fbd735886dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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150 <param name="gtf_source_select" value="cached"/>
4fbd735886dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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151 <param name="pdf" value=""/>
4fbd735886dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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152 <output name="out_tab" ftype="interval" file="outint.int" />
4fbd735886dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 853e74181667ce9ac6a0c91d4a2b204c0b3fda06
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153 </test>
0
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154 </tests>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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155 <help><![CDATA[
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156
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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157 .. class:: infomark
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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158
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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159 **What it does**
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160
2
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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161 ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the peak to the TSS of its nearest gene. Users can define the TSS (transcription start site) region under **Advanced Options**, by default the TSS region is defined from -3kb to +3kb. The genomic region of the peak is reported in the annotation column. Since some annotations may overlap for a peak, ChIPseeker adopts the following priority in genomic annotation:
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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162
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163 * Promoter
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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164 * 5’ UTR
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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165 * 3’ UTR
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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166 * Exon
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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167 * Intron
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168 * Downstream
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169 * Intergenic
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170
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171 ChIPseeker also produces plots to help users visualise the overlaps in annotation for peaks, for example, the vennpie and upsetplot. See the `ChIPseeker vignette`_ for more information.
0
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172
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173 -----
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174
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175 **Inputs**
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176
2
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177 A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind.
1
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178
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179 Example:
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180
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181 ===== ====== ====== ======== ===== ======
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182 Chrom Start End Name Score Strand
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183 ===== ====== ====== ======== ===== ======
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184 18 394599 396513 DiffBind 0 .
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185 18 111566 112005 DiffBind 0 .
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186 18 346463 347342 DiffBind 0 .
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187 18 399013 400382 DiffBind 0 .
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188 18 371109 372102 DiffBind 0 .
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189 ===== ====== ====== ======== ===== ======
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190
2
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191 A GTF file for annotation. The GTF file must have fields called "gene_id" and gene_name".
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192
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193 -----
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194
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195 **Outputs**
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196
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197 This tool outputs
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198
1
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199 * a file of annotated peaks in Interval or Tabular format
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200 * a PDF of plots (plotAnnoPie, vennpie, upsetplot)
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201
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202 Optionally, you can choose to output
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203
0
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204 * the R script used by this tool
2
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205 * an RData file
0
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206
1
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207 **Annotated peaks**
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208
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209 Annotation similar to below will be added to the input file.
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210
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211 Example - **Interval format**:
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212
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213 ===== ====== ====== =====================================================================================================================================================
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214 Chrom Start End Comment
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215 ===== ====== ====== =====================================================================================================================================================
2
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216 18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256| 3869|COLEC12|ENSG00000158270
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217 18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENST00000400256|53040|COLEC12|ENSG00000158270
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218 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENST00000400256| 0|COLEC12|ENSG00000158270
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219 18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256|28280|COLEC12|ENSG00000158270
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220 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENST00000608049| 0|ROCK1P1|ENSG00000263006
1
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221 ===== ====== ====== =====================================================================================================================================================
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222
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223 Columns contain the following data:
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224
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225 * **Chrom**: Chromosome name
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226 * **Start**: Start position of site
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227 * **End**: End position of site
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228 * **Comment**: The pipe ("|") separated values in this column correspond to:
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229
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230 * *<Any additional input columns>*
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231 * *annotation* (Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic)
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232 * *geneChr*
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233 * *geneStart*
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234 * *geneEnd*
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235 * *geneLength*
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236 * *geneStrand*
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237 * *transcriptId*
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238 * *distanceToTSS*
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239 * *geneName*
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240 * *geneId*
1
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241
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242 Example - **Tabular format**:
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243
2
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244 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
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245 Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS geneName geneId
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246 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
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247 18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 3869 COLEC12 ENSG00000158270
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248 18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENST00000400256 53040 COLEC12 ENSG00000158270
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249 18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENST00000400256 0 COLEC12 ENSG00000158270
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250 18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 28280 COLEC12 ENSG00000158270
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251 18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENST00000608049 0 ROCK1P1 ENSG00000263006
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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252 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
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2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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253
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313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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254 .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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255 .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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256
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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257 ]]></help>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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258 <citations>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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259 <citation type="doi">10.1093/bioinformatics/btv145</citation>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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260 </citations>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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261 </tool>