annotate ceas_wrapper.xml @ 4:cd6a48ffd093 draft default tip

Uploaded version 1.0.2-4.
author pjbriggs
date Wed, 26 Sep 2018 08:03:10 -0400
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1 <tool id="ceas" name="CEAS" version="1.0.2-4">
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2 <description>Annotate intervals and scores with genome features</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.2b1">cistrome-ceas</requirement>
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5 <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
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6 <requirement type="package" version="3.5.0">R</requirement>
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7 </requirements>
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8 <version_command>ceas --version 2&gt;&amp;1 | tail -1</version_command>
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9 <command><![CDATA[
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10 bash $__tool_directory__/ceas_wrapper.sh
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11 $bed_file ${gdb_file.fields.path}
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12 $log_output $pdf_report $xls_output
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13 #if (str($wig_file) != 'None')
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14 #if (str($wig_file.ext) == 'bigwig')
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15 --bigwig $wig_file
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16 --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
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17 #else
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18 --wig $wig_file
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19 #end if
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20 #end if
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21 #if (str($extra_bed_file) != 'None')
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22 --ebed $extra_bed_file
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23 #end if
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24 #if (str($span) and int(str($span)) > 0)
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25 --span $span
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26 #end if
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27 --sizes $sizes_lower,$sizes_middle,$sizes_upper
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28 --bisizes $bisizes_lower,$bisizes_upper
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29 --pf-res $profiling_resolution
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30 --rel-dist $relative_distance
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31 ]]></command>
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32 <inputs>
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33 <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" />
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34 <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true"
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35 help="If not supplied then only perform ChIP region annotation and gene-centered annotation" />
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36 <param name="extra_bed_file" type="data" format="bed" label="BED file with extra regions of interest (e.g. non-coding regions)" optional="true" />
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37 <param name="gdb_file" type="select" label="Gene annotation table">
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38 <options from_data_table="ceas_annotations">
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39 </options>
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40 <filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="1" />
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41 <validator type="no_options" message="No tables are available for the selected input"/>
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42 </param>
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43 <param name="span" type="integer"
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44 label="Span from TSS and TTS in the gene-centered annotation (bp)"
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45 help="ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates of promoter and downstream by ChIP regions (--span)" value="3000" />
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46 <param name="sizes_lower" type="integer"
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47 label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)"
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48 value="1000" help=" (--sizes)" />
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49 <param name="sizes_middle" type="integer"
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50 label="Middle interval for promoter/downstream sizes (bp)" value="2000"
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51 help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
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52 <param name="sizes_upper" type="integer"
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53 label="Upper interval for promoter/downstream sizes (bp)" value="3000"
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54 help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
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55 <param name="bisizes_lower" type="integer"
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56 label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500"
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57 help="(--bisizes)" />
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58 <param name="bisizes_upper" type="integer"
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59 label="Upper interval for bidirectional-promoter sizes (bp)" value="5000"
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60 help="Values > 20000bp are automatically fixed to 20000bp (--bisizes)" />
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61 <param name="profiling_resolution" type="integer"
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62 label="Wig profiling resolution (bp)" value="50"
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63 help="Warning: a number smaller than the wig interval (resolution) may cause aliasing error (--pf-res)" />
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64 <param name="relative_distance" type="integer"
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65 label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000"
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66 help="(--rel-dist)" />
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67 </inputs>
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68 <outputs>
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69 <data name="log_output" format="txt" label="CEAS on ${on_string} (log output)" />
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70 <data name="pdf_report" format="pdf" label="CEAS on ${on_string} (PDF report)" />
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71 <data name="xls_output" format="interval" label="CEAS on ${on_string} (XLS output)" />
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72 </outputs>
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73 <tests>
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74 <test>
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75 <!-- Test with bed input only -->
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76 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
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77 <param name="gdb_file" value="galGal3_test" />
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78 <output name="log_output" file="ceas_out1.log.re_match" compare="re_match"/>
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79 <output name="pdf_report" file="ceas_out1.pdf" />
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80 <output name="xls_output" file="ceas_out1.xls" />
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81 </test>
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82 <test>
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83 <!-- Test with bed & very small wig input -->
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84 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
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85 <param name="wig_file" value="ceas_in.wig" ftype="wig" />
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86 <param name="gdb_file" value="galGal3_test" />
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87 <output name="log_output" file="ceas_out2.log.re_match" compare="re_match"/>
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88 <output name="pdf_report" file="ceas_out2.pdf" />
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89 <output name="xls_output" file="ceas_out2.xls" />
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90 </test>
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91 <test>
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92 <!-- Test with bed & bigwig input -->
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93 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
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94 <param name="wig_file" value="ceas_in.bigwig" ftype="bigwig" />
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95 <param name="gdb_file" value="galGal3_test" />
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96 <output name="log_output" file="ceas_out3.log.re_match" compare="re_match"/>
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97 <output name="pdf_report" file="ceas_out3.pdf" />
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98 <output name="xls_output" file="ceas_out3.xls" />
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99 </test>
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100 </tests>
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101 <help>
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102 **What it does**
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103
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104 CEAS (Cis-regulatory Element Annotation System) is a tool for characterizing genome-wide
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105 protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad
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106 binding factors. It provides statistics on ChIP enrichment at important genome features
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107 such as specific chromosome, promoters, gene bodies, or exons, and infers genes most
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108 likely to be regulated by a binding factor.
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109
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110 CEAS also enables biologists to visualize the average ChIP enrichment signals over
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111 specific genomic features, allowing continuous and broad ChIP enrichment to be perceived
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112 which might be too subtle to detect from ChIP peaks alone.
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113
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114 **Usage**
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115
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116 CEAS takes the following inputs:
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117
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118 * BED file with discrete ChIP regions (for example, the 'summits' output from the MACS
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119 peak caller)
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120 * WIG or bigWIG file with a continuous ChIP enrichment signal
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121 * Gene annotation table (provided as reference data)
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122
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123 Optionally it can also take a BED file describing extra regions of interest (for example
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124 non-coding regions).
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125
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126 The analysis modules are:
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127
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128 * **ChIP region annotation:** estimates the relative enrichment level of ChIP regions in
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129 each gene feature with respect to the whole genome.
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130 * **Gene-centered annotation:** identifies genes associated with ChIP regions to infer
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131 the direct regulatory gene targets of the binding factor of interest.
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132 * **Average signal profiling within/near important genomic features:** displays continuous
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133 ChIP enrichment signal within/around important gene features to help visualize the
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134 average binding patterns.
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135
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136 **Background**
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137
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138 This tool is compatible with the ceasBW version of CEAS from the Cistrome package
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139 obtained from
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140
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141 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
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142
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143 (commit id d8c0751, datestamp 20140929). The CEAS code is under the
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144 published-packages/CEAS/ subdirectory.
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145
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146 Cistrome data files and documentation can be found at
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147
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148 http://liulab.dfci.harvard.edu/CEAS/index.html
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149
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150 The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html
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151 </help>
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152 <citations>
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153 <!--
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154 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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155 Can be either DOI or Bibtex
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156 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
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157 -->
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158 <citation type="doi">10.1093/bioinformatics/btp479</citation>
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159 </citations>
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160 </tool>