Mercurial > repos > rnateam > chipseeker

annotate chipseeker.xml @ 6:b418a1d3585d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
author rnateam
date Wed, 13 Mar 2019 03:05:16 -0400
parents 4c2dbe4dbb4e
children 1b9a9409831d
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b418a1d3585d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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1 <tool id="chipseeker" name="ChIPseeker" version="1.18.0">
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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="1.18.0">bioconductor-chipseeker</requirement>
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5 <requirement type="package" version="1.6.1">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 &&
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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 &&
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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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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
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29 #if $adv.flankgeneinfo:
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30 -F $adv.flankgeneinfo
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31 #end if
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33 -D $adv.flankgenedist
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35 #if $adv.ignoreUpstream:
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36 -j $adv.ignoreUpstream
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37 #end if
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39 #if $adv.ignoreDownstream:
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40 -k $adv.ignoreDownstream
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41 #end if
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42
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43 -f $format
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44
5
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45 #if $pdf:
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46 -p $pdf
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47 #end if
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48
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49 -r $rdata
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50 ]]>
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51 </command>
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52 <inputs>
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53 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
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54 <conditional name="gtf_source">
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55 <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
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56 <option value="cached" selected="true">Use a built-in GTF</option>
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57 <option value="history">Use a GTF from history</option>
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58 </param>
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59 <when value="cached">
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60 <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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61 <options from_data_table="gene_sets">
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62 <filter type="sort_by" column="2" />
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63 <validator type="no_options" message="No GTF file is available." />
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64 </options>
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65 </param>
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66 </when>
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67 <when value="history">
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68 <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" />
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69 </when>
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70 </conditional>
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71 <param name="format" type="select" label="Output Format">
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72 <option value="interval" selected="True">Interval</option>
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73 <option value="tabular">Tabular (tab-separated)</option>
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74 </param>
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75 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />
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76 <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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77 <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"
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78 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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79 </param>
2
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80
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81 <section name="adv" expanded="false" title="Advanced Options">
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82 <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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83 <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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84 <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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85 <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."/>
6
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86 <param name="ignoreUpstream" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Ignore upstream?" help="If Yes only annotate gene at the 3’ of the peak. Default: No."/>
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87 <param name="ignoreDownstream" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Ignore downstream?" help="If Yes only annotate gene at the 5’ of the peak. Default: No."/>
2
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88 </section>
0
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89 </inputs>
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90
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91 <outputs>
1
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92 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >
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93 <change_format>
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94 <when input="format" value="tabular" format="tabular" />
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95 </change_format>
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96 </data>
0
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97 <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots">
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98 <filter>pdf</filter>
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99 </data>
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100 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
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101 <filter>rscript</filter>
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102 </data>
3
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103 <data name="out_rdata" format="rdata" from_work_dir="ChIPseeker_analysis.RData" label="${tool.name} on ${on_string}: RData file">
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104 <filter>rdata</filter>
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105 </data>
0
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106 </outputs>
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107
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108 <tests>
1
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109 <!-- Ensure bed and GTF inputs and all outputs work -->
3
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110 <test expect_num_outputs="4">
1
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111 <param name="peaks" value="in.bed" ftype="bed"/>
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112 <param name="gtf_source_select" value="history"/>
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113 <param name="gtf_hist" value="in.gtf"/>
0
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114 <param name="rscript" value="True"/>
3
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115 <param name="rdata" value="True"/>
1
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116 <output name="out_tab" ftype="interval" file="out.int" />
0
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117 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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118 <output name="out_rscript" >
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119 <assert_contents>
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120 <has_text_matching expression="peakAnno.*annotatePeak" />
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121 </assert_contents>
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122 </output>
3
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123 <output name="out_rdata" file="out.rdata" compare="sim_size" />
0
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124 </test>
1
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125 <!-- Ensure built-in GTF works -->
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126 <test expect_num_outputs="2">
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127 <param name="peaks" value="in.interval" ftype="interval"/>
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128 <param name="gtf_source_select" value="cached"/>
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129 <output name="out_tab" ftype="interval" file="outint.int" />
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130 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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131 </test>
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132 <!-- Ensure tabular output works -->
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133 <test expect_num_outputs="2">
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134 <param name="peaks" value="in.interval" ftype="interval"/>
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135 <param name="gtf_source_select" value="history"/>
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136 <param name="gtf_hist" value="in.gtf"/>
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137 <param name="format" value="tabular"/>
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138 <output name="out_tab" ftype="tabular" file="outint.tab" />
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139 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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140 </test>
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141 <!-- Ensure TSS region specification works -->
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142 <test expect_num_outputs="2">
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143 <param name="peaks" value="in.interval" ftype="interval"/>
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144 <param name="gtf_source_select" value="history"/>
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145 <param name="gtf_hist" value="in.gtf"/>
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146 <param name="upstream" value="1000" />
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147 <param name="downstream" value="1000" />
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148 <param name="format" value="tabular"/>
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149 <output name="out_tab" ftype="tabular" file="outtss.tab" />
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150 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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151 </test>
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152 <!-- Ensure flanking genes works -->
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153 <test expect_num_outputs="2">
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154 <param name="peaks" value="in.interval" ftype="interval"/>
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155 <param name="gtf_source_select" value="history"/>
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156 <param name="gtf_hist" value="in.gtf"/>
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157 <param name="flankgeneinfo" value="True" />
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158 <param name="format" value="tabular"/>
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159 <output name="out_tab" ftype="tabular" file="outflank.tab" />
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160 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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161 </test>
5
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162 <!-- Ensure the tool works when no plots are outputed -->
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163 <test expect_num_outputs="1">
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164 <param name="peaks" value="in.interval" ftype="interval"/>
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165 <param name="gtf_source_select" value="cached"/>
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166 <param name="pdf" value=""/>
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167 <output name="out_tab" ftype="interval" file="outint.int" />
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168 </test>
0
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169 </tests>
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170 <help><![CDATA[
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171
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172 .. class:: infomark
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173
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174 **What it does**
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175
2
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176 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:
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177
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178 * Promoter
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179 * 5’ UTR
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180 * 3’ UTR
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181 * Exon
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182 * Intron
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183 * Downstream
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184 * Intergenic
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185
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186 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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187
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188 -----
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189
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190 **Inputs**
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191
2
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192 A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind.
1
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193
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194 Example:
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195
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196 ===== ====== ====== ======== ===== ======
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197 Chrom Start End Name Score Strand
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198 ===== ====== ====== ======== ===== ======
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199 18 394599 396513 DiffBind 0 .
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200 18 111566 112005 DiffBind 0 .
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201 18 346463 347342 DiffBind 0 .
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202 18 399013 400382 DiffBind 0 .
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203 18 371109 372102 DiffBind 0 .
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204 ===== ====== ====== ======== ===== ======
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205
3
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206 A GTF file for annotation. The GTF file must have fields called "gene_id" and gene_name".
0
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207
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208 -----
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209
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210 **Outputs**
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211
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212 This tool outputs
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213
1
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214 * a file of annotated peaks in Interval or Tabular format
2
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215 * a PDF of plots (plotAnnoPie, vennpie, upsetplot)
3
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216
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217 Optionally, you can choose to output
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218
0
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219 * the R script used by this tool
3
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220 * an RData file
0
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221
1
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222 **Annotated peaks**
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223
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224 Annotation similar to below will be added to the input file.
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225
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226 Example - **Interval format**:
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227
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228 ===== ====== ====== =====================================================================================================================================================
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229 Chrom Start End Comment
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230 ===== ====== ====== =====================================================================================================================================================
3
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231 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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232 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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233 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENST00000400256| 0|COLEC12|ENSG00000158270
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234 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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235 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENST00000608049| 0|ROCK1P1|ENSG00000263006
1
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236 ===== ====== ====== =====================================================================================================================================================
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237
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238 Columns contain the following data:
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239
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240 * **Chrom**: Chromosome name
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241 * **Start**: Start position of site
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242 * **End**: End position of site
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243 * **Comment**: The pipe ("|") separated values in this column correspond to:
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244
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245 * *<Any additional input columns>*
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246 * *annotation* (Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic)
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247 * *geneChr*
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248 * *geneStart*
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249 * *geneEnd*
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250 * *geneLength*
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251 * *geneStrand*
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252 * *transcriptId*
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253 * *distanceToTSS*
3
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254 * *geneName*
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255 * *geneId*
1
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256
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257 Example - **Tabular format**:
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258
3
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259 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
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260 Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS geneName geneId
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261 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
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262 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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263 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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264 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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265 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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266 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
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267 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
1
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268
0
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269 .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
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270 .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
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271
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272 ]]></help>
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273 <citations>
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274 <citation type="doi">10.1093/bioinformatics/btv145</citation>
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275 </citations>
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276 </tool>