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annotate chipseeker.xml @ 1:2019b4dd86a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
author rnateam
date Tue, 29 May 2018 15:07:04 -0400
parents 313332cb7745
children 195cba35110e
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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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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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2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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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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2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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11 #set gtf = "refgtf"
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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12 #if $gtf_source.gtf_source_select == "history":
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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13 ln -s '${gtf_source.gtf_hist}' $gtf &&
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'
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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23
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24 -i '$peaks'
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25 -G '$gtf'
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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26 -u $upstream
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27 -d $downstream
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28 #if $flankgeneinfo:
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29 -F $flankgeneinfo
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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30 -D $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>
1
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37 <param name="peaks" type="data" format="bed,interval" label="Peaks file" help="A peaks file in BED format." />
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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38 <conditional name="gtf_source">
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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39 <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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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>
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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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="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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56 <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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57 <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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58 <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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59 <param name="format" type="select" label="Output Format">
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60 <option value="interval" selected="True">Interval</option>
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61 <option value="tabular">Tabular (tab-separated)</option>
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62 </param>
1
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63 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />
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64 <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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65 </inputs>
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66
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67 <outputs>
1
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68 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >
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69 <change_format>
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70 <when input="format" value="tabular" format="tabular" />
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71 </change_format>
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72 </data>
0
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73 <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots">
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74 <filter>pdf</filter>
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75 </data>
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76 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
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77 <filter>rscript</filter>
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78 </data>
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79 </outputs>
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80
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81 <tests>
1
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82 <!-- Ensure bed and GTF inputs and all outputs work -->
0
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83 <test expect_num_outputs="3">
1
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84 <param name="peaks" value="in.bed" ftype="bed"/>
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85 <param name="gtf_source_select" value="history"/>
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86 <param name="gtf_hist" value="in.gtf"/>
0
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87 <param name="rscript" value="True"/>
1
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88 <output name="out_tab" ftype="interval" file="out.int" />
0
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89 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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90 <output name="out_rscript" >
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91 <assert_contents>
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92 <has_text_matching expression="peakAnno.*annotatePeak" />
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93 </assert_contents>
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94 </output>
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95 </test>
1
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96 <!-- Ensure built-in GTF works -->
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97 <test expect_num_outputs="2">
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98 <param name="peaks" value="in.interval" ftype="interval"/>
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99 <param name="gtf_source_select" value="cached"/>
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100 <output name="out_tab" ftype="interval" file="outint.int" />
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101 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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102 </test>
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103 <!-- Ensure tabular output works -->
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104 <test expect_num_outputs="2">
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105 <param name="peaks" value="in.interval" ftype="interval"/>
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106 <param name="gtf_source_select" value="history"/>
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107 <param name="gtf_hist" value="in.gtf"/>
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108 <param name="format" value="tabular"/>
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109 <output name="out_tab" ftype="tabular" file="outint.tab" />
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110 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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111 </test>
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112 <!-- Ensure TSS region specification works -->
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113 <test expect_num_outputs="2">
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114 <param name="peaks" value="in.interval" ftype="interval"/>
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115 <param name="gtf_source_select" value="history"/>
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116 <param name="gtf_hist" value="in.gtf"/>
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117 <param name="upstream" value="1000" />
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118 <param name="downstream" value="1000" />
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119 <param name="format" value="tabular"/>
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120 <output name="out_tab" ftype="tabular" file="outtss.tab" />
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121 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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122 </test>
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123 <!-- Ensure flanking genes works -->
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124 <test expect_num_outputs="2">
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125 <param name="peaks" value="in.interval" ftype="interval"/>
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126 <param name="gtf_source_select" value="history"/>
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127 <param name="gtf_hist" value="in.gtf"/>
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128 <param name="flankgeneinfo" value="True" />
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129 <param name="format" value="tabular"/>
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130 <output name="out_tab" ftype="tabular" file="outflank.tab" />
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131 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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132 </test>
0
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133 </tests>
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134 <help><![CDATA[
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135
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136 .. class:: infomark
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137
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138 **What it does**
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139
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140 ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. See
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141 the `ChIPseeker vignette`_ for more information.
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142
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143 -----
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144
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145 **Inputs**
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146
1
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147 A peaks file in BED or Interval format e.g from MACS2 or DiffBind.
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148
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149 Example:
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150
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151 ===== ====== ====== ======== ===== ======
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152 Chrom Start End Name Score Strand
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153 ===== ====== ====== ======== ===== ======
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154 18 394599 396513 DiffBind 0 .
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155 18 111566 112005 DiffBind 0 .
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156 18 346463 347342 DiffBind 0 .
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157 18 399013 400382 DiffBind 0 .
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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158 18 371109 372102 DiffBind 0 .
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159 ===== ====== ====== ======== ===== ======
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160
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161 A GTF file for annotation.
0
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162
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163 -----
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164
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165 **Outputs**
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166
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167 This tool outputs
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168
1
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169 * a file of annotated peaks in Interval or Tabular format
0
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170 * a PDF of plots
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171 * the R script used by this tool
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172
1
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173 **Annotated peaks**
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174
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175 Annotation similar to below will be added to the input file.
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176
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177 Example - **Interval format**:
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178
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179 ===== ====== ====== =====================================================================================================================================================
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180 Chrom Start End Comment
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181 ===== ====== ====== =====================================================================================================================================================
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182 18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 3869
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183 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENSG00000263006|ENST00000608049| 0
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184 18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|53040
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185 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 0
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186 18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|28280
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187 ===== ====== ====== =====================================================================================================================================================
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188
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189 Columns contain the following data:
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190
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191 * **Chrom**: Chromosome name
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192 * **Start**: Start position of site
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193 * **End**: End position of site
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194 * **Comment**: The pipe ("|") separated values in this column correspond to:
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195
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196 * *<Any additional input columns>*
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197 * *annotation* (Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic)
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198 * *geneChr*
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199 * *geneStart*
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200 * *geneEnd*
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201 * *geneLength*
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202 * *geneStrand*
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203 * *geneId*
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204 * *transcriptId*
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205 * *distanceToTSS*
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206
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207 Example - **Tabular format**:
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208
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209 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== =============
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210 Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand geneId transcriptId distanceToTSS
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211 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== =============
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212 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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213 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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214 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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215 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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216 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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217 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== =============
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218
0
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219 .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
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220 .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
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221
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222 ]]></help>
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223 <citations>
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224 <citation type="doi">10.1093/bioinformatics/btv145</citation>
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225 </citations>
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226 </tool>