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annotate chipseeker.xml @ 2:cb133602cd9b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
author rnateam
date Wed, 30 May 2018 06:12:27 -0400
parents 95f779f4adb7
children 535321abf9a4
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1 <tool id="chipseeker" name="ChIPseeker" version="1.14.2.1">
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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="1.14.2">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 $gtf_source.gtf_source_select == "history":
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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13 ln -s '${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
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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 #if $adv.flankgeneinfo:
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29 -F $adv.flankgeneinfo
cb133602cd9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
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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 -p $pdf
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34 ]]>
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35 </command>
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36 <inputs>
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37 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
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38 <conditional name="gtf_source">
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39 <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
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40 <option value="cached" selected="true">Use a built-in GTF</option>
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41 <option value="history">Use a GTF from history</option>
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42 </param>
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43 <when value="cached">
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44 <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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45 <options from_data_table="gene_sets">
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46 <filter type="sort_by" column="2" />
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47 <validator type="no_options" message="No GTF file is available." />
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48 </options>
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49 </param>
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50 </when>
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51 <when value="history">
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52 <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" />
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53 </when>
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54 </conditional>
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55 <param name="format" type="select" label="Output Format">
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56 <option value="interval" selected="True">Interval</option>
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57 <option value="tabular">Tabular (tab-separated)</option>
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58 </param>
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59 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />
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60 <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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61
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62 <section name="adv" expanded="false" title="Advanced Options">
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63 <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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64 <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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65 <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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66 <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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67 </section>
0
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68 </inputs>
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69
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70 <outputs>
1
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71 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >
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72 <change_format>
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73 <when input="format" value="tabular" format="tabular" />
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74 </change_format>
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75 </data>
0
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76 <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots">
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77 <filter>pdf</filter>
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78 </data>
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79 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
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80 <filter>rscript</filter>
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81 </data>
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82 </outputs>
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83
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84 <tests>
1
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85 <!-- Ensure bed and GTF inputs and all outputs work -->
0
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86 <test expect_num_outputs="3">
1
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87 <param name="peaks" value="in.bed" ftype="bed"/>
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88 <param name="gtf_source_select" value="history"/>
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89 <param name="gtf_hist" value="in.gtf"/>
0
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90 <param name="rscript" value="True"/>
1
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91 <output name="out_tab" ftype="interval" file="out.int" />
0
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92 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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93 <output name="out_rscript" >
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94 <assert_contents>
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95 <has_text_matching expression="peakAnno.*annotatePeak" />
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96 </assert_contents>
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97 </output>
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98 </test>
1
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99 <!-- Ensure built-in GTF works -->
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100 <test expect_num_outputs="2">
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101 <param name="peaks" value="in.interval" ftype="interval"/>
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102 <param name="gtf_source_select" value="cached"/>
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103 <output name="out_tab" ftype="interval" file="outint.int" />
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104 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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105 </test>
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106 <!-- Ensure tabular output works -->
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107 <test expect_num_outputs="2">
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108 <param name="peaks" value="in.interval" ftype="interval"/>
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109 <param name="gtf_source_select" value="history"/>
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110 <param name="gtf_hist" value="in.gtf"/>
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111 <param name="format" value="tabular"/>
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112 <output name="out_tab" ftype="tabular" file="outint.tab" />
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113 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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114 </test>
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115 <!-- Ensure TSS region specification works -->
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116 <test expect_num_outputs="2">
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117 <param name="peaks" value="in.interval" ftype="interval"/>
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118 <param name="gtf_source_select" value="history"/>
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119 <param name="gtf_hist" value="in.gtf"/>
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120 <param name="upstream" value="1000" />
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121 <param name="downstream" value="1000" />
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122 <param name="format" value="tabular"/>
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123 <output name="out_tab" ftype="tabular" file="outtss.tab" />
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124 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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125 </test>
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126 <!-- Ensure flanking genes works -->
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127 <test expect_num_outputs="2">
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128 <param name="peaks" value="in.interval" ftype="interval"/>
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129 <param name="gtf_source_select" value="history"/>
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130 <param name="gtf_hist" value="in.gtf"/>
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131 <param name="flankgeneinfo" value="True" />
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132 <param name="format" value="tabular"/>
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133 <output name="out_tab" ftype="tabular" file="outflank.tab" />
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134 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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135 </test>
0
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136 </tests>
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137 <help><![CDATA[
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138
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139 .. class:: infomark
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140
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141 **What it does**
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142
2
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143 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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144
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145 * Promoter
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146 * 5’ UTR
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147 * 3’ UTR
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148 * Exon
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149 * Intron
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150 * Downstream
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151 * Intergenic
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152
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153 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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154
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155 -----
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156
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157 **Inputs**
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158
2
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159 A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind.
1
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160
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161 Example:
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162
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163 ===== ====== ====== ======== ===== ======
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164 Chrom Start End Name Score Strand
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165 ===== ====== ====== ======== ===== ======
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166 18 394599 396513 DiffBind 0 .
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167 18 111566 112005 DiffBind 0 .
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168 18 346463 347342 DiffBind 0 .
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169 18 399013 400382 DiffBind 0 .
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170 18 371109 372102 DiffBind 0 .
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171 ===== ====== ====== ======== ===== ======
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172
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173 A GTF file for annotation.
0
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174
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175 -----
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176
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177 **Outputs**
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178
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179 This tool outputs
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180
1
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181 * a file of annotated peaks in Interval or Tabular format
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182 * a PDF of plots (plotAnnoPie, vennpie, upsetplot)
0
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183 * the R script used by this tool
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184
1
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185 **Annotated peaks**
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186
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187 Annotation similar to below will be added to the input file.
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188
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189 Example - **Interval format**:
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190
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191 ===== ====== ====== =====================================================================================================================================================
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192 Chrom Start End Comment
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193 ===== ====== ====== =====================================================================================================================================================
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194 18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 3869
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195 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENSG00000263006|ENST00000608049| 0
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196 18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|53040
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197 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 0
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198 18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|28280
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199 ===== ====== ====== =====================================================================================================================================================
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200
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201 Columns contain the following data:
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202
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203 * **Chrom**: Chromosome name
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204 * **Start**: Start position of site
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205 * **End**: End position of site
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206 * **Comment**: The pipe ("|") separated values in this column correspond to:
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207
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208 * *<Any additional input columns>*
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209 * *annotation* (Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic)
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210 * *geneChr*
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211 * *geneStart*
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212 * *geneEnd*
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213 * *geneLength*
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214 * *geneStrand*
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215 * *geneId*
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216 * *transcriptId*
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217 * *distanceToTSS*
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218
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219 Example - **Tabular format**:
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220
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221 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== =============
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222 Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand geneId transcriptId distanceToTSS
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223 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== =============
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224 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 ENSG00000158270 ENST00000400256 3869
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225 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 ENSG00000263006 ENST00000608049 0
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226 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 ENSG00000158270 ENST00000400256 53040
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227 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 ENSG00000158270 ENST00000400256 0
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228 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 ENSG00000158270 ENST00000400256 28280
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229 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== =============
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230
0
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231 .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
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232 .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
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233
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234 ]]></help>
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235 <citations>
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236 <citation type="doi">10.1093/bioinformatics/btv145</citation>
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237 </citations>
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238 </tool>