Mercurial > repos > rnateam > chipseeker

annotate chipseeker.xml @ 8:8bd92f2404dd draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
author rnateam
date Fri, 27 Aug 2021 10:49:39 +0000
parents 1b9a9409831d
children
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8bd92f2404dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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1 <tool id="chipseeker" name="ChIPseeker" version="1.28.3+galaxy0">
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2 <description>for ChIP peak annotation and visualization</description>
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3 <requirements>
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8bd92f2404dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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4 <requirement type="package" version="1.28.3">bioconductor-chipseeker</requirement>
8bd92f2404dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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5 <requirement type="package" version="1.6.6">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 -H $header
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26 -G '$gtf'
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27 -u $adv.upstream
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28 -d $adv.downstream
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29
2
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30 #if $adv.flankgeneinfo:
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31 -F $adv.flankgeneinfo
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32 #end if
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34 -D $adv.flankgenedist
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36 #if $adv.ignoreUpstream:
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37 -j $adv.ignoreUpstream
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38 #end if
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40 #if $adv.ignoreDownstream:
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41 -k $adv.ignoreDownstream
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42 #end if
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43
1
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44 -f $format
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45
5
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46 #if $pdf:
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47 -p $pdf
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48 #end if
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49
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50 -r $rdata
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51 ]]>
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52 </command>
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53 <inputs>
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54 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
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55 <param name="header" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Peaks file has header?" help="If this option is set to Yes, the tool will assume that the peak file has column headers in the first row. Default: No" />
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56 <conditional name="gtf_source">
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57 <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
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58 <option value="cached" selected="true">Use a built-in GTF</option>
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59 <option value="history">Use a GTF from history</option>
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60 </param>
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61 <when value="cached">
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62 <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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63 <options from_data_table="gene_sets">
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64 <filter type="sort_by" column="2" />
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65 <validator type="no_options" message="No GTF file is available." />
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66 </options>
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67 </param>
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68 </when>
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69 <when value="history">
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70 <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" />
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71 </when>
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72 </conditional>
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73 <param name="format" type="select" label="Output Format">
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74 <option value="interval" selected="True">Interval</option>
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75 <option value="tabular">Tabular (tab-separated)</option>
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76 </param>
1
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77 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />
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78 <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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79 <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"
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80 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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81 </param>
2
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82
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83 <section name="adv" expanded="false" title="Advanced Options">
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84 <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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85 <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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86 <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."/>
cb133602cd9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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87 <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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88 <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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89 <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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90 </section>
0
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91 </inputs>
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92
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93 <outputs>
1
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94 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >
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95 <change_format>
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96 <when input="format" value="tabular" format="tabular" />
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97 </change_format>
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98 </data>
0
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99 <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots">
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100 <filter>pdf</filter>
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101 </data>
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102 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
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103 <filter>rscript</filter>
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104 </data>
3
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105 <data name="out_rdata" format="rdata" from_work_dir="ChIPseeker_analysis.RData" label="${tool.name} on ${on_string}: RData file">
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106 <filter>rdata</filter>
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107 </data>
0
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108 </outputs>
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109
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110 <tests>
1
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111 <!-- Ensure bed and GTF inputs and all outputs work -->
3
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112 <test expect_num_outputs="4">
1
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113 <param name="peaks" value="in.bed" ftype="bed"/>
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114 <param name="gtf_source_select" value="history"/>
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115 <param name="gtf_hist" value="in.gtf"/>
0
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116 <param name="rscript" value="True"/>
3
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117 <param name="rdata" value="True"/>
1
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118 <output name="out_tab" ftype="interval" file="out.int" />
0
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119 <output name="out_plots" file="out.pdf" compare="sim_size"/>
8
8bd92f2404dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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120 <output name="out_rscript">
0
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121 <assert_contents>
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8bd92f2404dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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122 <has_text_matching expression="peak_anno.*annotatePeak" />
0
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123 </assert_contents>
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124 </output>
8
8bd92f2404dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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125 <output name="out_rdata">
8bd92f2404dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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126 <assert_contents>
8bd92f2404dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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127 <has_size value="160346" delta="300"/>
8bd92f2404dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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128 </assert_contents>
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129 </output>
0
58ef4507ce5a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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130 </test>
1
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131 <!-- Ensure built-in GTF works -->
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132 <test expect_num_outputs="2">
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133 <param name="peaks" value="in.interval" ftype="interval"/>
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134 <param name="gtf_source_select" value="cached"/>
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135 <output name="out_tab" ftype="interval" file="outint.int" />
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136 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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137 </test>
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138 <!-- Ensure tabular output works -->
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139 <test expect_num_outputs="2">
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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140 <param name="peaks" value="in.interval" ftype="interval"/>
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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141 <param name="gtf_source_select" value="history"/>
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142 <param name="gtf_hist" value="in.gtf"/>
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143 <param name="format" value="tabular"/>
95f779f4adb7 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="outint.tab" />
95f779f4adb7 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"/>
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146 </test>
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147 <!-- Ensure TSS region specification works -->
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148 <test expect_num_outputs="2">
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149 <param name="peaks" value="in.interval" ftype="interval"/>
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150 <param name="gtf_source_select" value="history"/>
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151 <param name="gtf_hist" value="in.gtf"/>
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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152 <param name="upstream" value="1000" />
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153 <param name="downstream" value="1000" />
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154 <param name="format" value="tabular"/>
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155 <output name="out_tab" ftype="tabular" file="outtss.tab" />
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156 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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157 </test>
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158 <!-- Ensure flanking genes works -->
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159 <test expect_num_outputs="2">
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160 <param name="peaks" value="in.interval" ftype="interval"/>
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161 <param name="gtf_source_select" value="history"/>
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162 <param name="gtf_hist" value="in.gtf"/>
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163 <param name="flankgeneinfo" value="True" />
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164 <param name="format" value="tabular"/>
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165 <output name="out_tab" ftype="tabular" file="outflank.tab" />
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166 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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167 </test>
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168 <!-- Ensure the tool works when no plots are outputed -->
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169 <test expect_num_outputs="1">
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170 <param name="peaks" value="in.interval" ftype="interval"/>
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171 <param name="gtf_source_select" value="cached"/>
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172 <param name="pdf" value=""/>
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173 <output name="out_tab" ftype="interval" file="outint.int" />
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174 </test>
0
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175 </tests>
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176 <help><![CDATA[
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177
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178 .. class:: infomark
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179
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180 **What it does**
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181
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182 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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183
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184 * Promoter
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185 * 5’ UTR
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186 * 3’ UTR
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187 * Exon
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188 * Intron
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189 * Downstream
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190 * Intergenic
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191
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192 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.
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193
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194 -----
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195
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196 **Inputs**
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197
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198 A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind. Note that there is an option to specify if the input peaks file has a header row. No header row is assumed by default, which is usually the case for BED format e.g. MACS narrowpeak, however other formats e.g. MACS tabular format, may contain a header row.
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199
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200 Example:
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201
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202 ===== ====== ====== ======== ===== ======
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203 Chrom Start End Name Score Strand
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204 ===== ====== ====== ======== ===== ======
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205 18 394599 396513 DiffBind 0 .
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206 18 111566 112005 DiffBind 0 .
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207 18 346463 347342 DiffBind 0 .
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208 18 399013 400382 DiffBind 0 .
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209 18 371109 372102 DiffBind 0 .
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210 ===== ====== ====== ======== ===== ======
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211
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212 A GTF file for annotation. The GTF file must have fields called "gene_id" and gene_name".
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213
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214 -----
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215
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216 **Outputs**
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217
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218 This tool outputs
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219
1
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220 * a file of annotated peaks in Interval or Tabular format
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221 * a PDF of plots (plotAnnoPie, plotAnnoBar, vennpie, upsetplot, plotDistToTSS)
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222
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223 Optionally, you can choose to output
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224
0
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225 * the R script used by this tool
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226 * an RData file
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227
1
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228 **Annotated peaks**
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229
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230 Annotation similar to below will be added to the input file.
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231
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232 Example - **Interval format**:
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233
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234 ===== ====== ====== =====================================================================================================================================================
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235 Chrom Start End Comment
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236 ===== ====== ====== =====================================================================================================================================================
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237 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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238 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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239 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENST00000400256| 0|COLEC12|ENSG00000158270
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240 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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241 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENST00000608049| 0|ROCK1P1|ENSG00000263006
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242 ===== ====== ====== =====================================================================================================================================================
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243
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244 Columns contain the following data:
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245
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246 * **Chrom**: Chromosome name
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247 * **Start**: Start position of site
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248 * **End**: End position of site
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249 * **Comment**: The pipe ("|") separated values in this column correspond to:
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250
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251 * *<Any additional input columns>*
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252 * *annotation* (Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic)
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253 * *geneChr*
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254 * *geneStart*
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255 * *geneEnd*
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256 * *geneLength*
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257 * *geneStrand*
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258 * *transcriptId*
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259 * *distanceToTSS*
3
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260 * *geneName*
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261 * *geneId*
1
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262
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263 Example - **Tabular format**:
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264
3
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265 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
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266 Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS geneName geneId
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267 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
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268 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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269 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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270 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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271 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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272 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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273 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
1
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274
0
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275 .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
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276 .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
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277
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278 ]]></help>
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279 <citations>
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280 <citation type="doi">10.1093/bioinformatics/btv145</citation>
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281 </citations>
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282 </tool>