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1 <tool id="ceas" name="CEAS" version="1.0.2">
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2 <description>Get stats on ChIP enrichment and infer genes regulated by binding factors</description>
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3
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4 <command>
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5 mkdir -p "$pdf_out.files_path" &&
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6 cd "$pdf_out.files_path" &&
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7
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8 ceas
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9
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10 -g "$refgene_table.fields.path"
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11 #if $analysis_files.wig_or_bed == "bed" or $analysis_files.wig_or_bed == "both1" or $analysis_files.wig_or_bed == "both2":
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12 -b $chip_bed
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13 #end if
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14
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15 #if $analysis_files.wig_or_bed == "wig" or $analysis_files.wig_or_bed == "both1" or $analysis_files.wig_or_bed == "both2":
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16 -w $chip_wig
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17 #end if
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18
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19 #if $analysis_files.wig_or_bed == "both2":
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20 --bg
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21 #end if
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22
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23 #if str($extra_bed) != 'None':
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24 -e $extra_bed
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25 #end if
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26
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27 #if str($sizes) != "":
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28 --sizes=$sizes
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29 #end if
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30
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31 #if str($bisizes) != "":
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32 --bisizes=$bisizes
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33 #end if
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34
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35 #if str($span) != "":
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36 --span=$span
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37 #end if
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38
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39 #if str($pfres) != "":
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40 --pf-res=$pfres
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41 #end if
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42
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43 #if str($reldist) != "":
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44 --rel-dist=$reldist
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45 #end if
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46
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47 --name=ceas_out
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48
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49 2> /dev/null
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50
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51 &&
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52
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53 #if $analysis_files.wig_or_bed != "wig":
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54 mv $pdf_out.files_path/ceas_out.xls $annot_out &&
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55 #end if
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56 mv $pdf_out.files_path/ceas_out.R $r_out &&
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57 mv $pdf_out.files_path/ceas_out.pdf $pdf_out &&
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58
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59 rm -r "$pdf_out.files_path"
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60 </command>
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61
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62 <inputs>
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63 <conditional name="analysis_files">
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64 <param name="wig_or_bed" type="select" optional="false" label="Select the type of analysis">
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65 <option value="bed" selected="true">Run only ChIP region and gene-centered annotation</option>
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66 <option value="wig">Run only average signal profiling</option>
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67 <option value="both1">Run both annotation and profiling</option>
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68 <option value="both2">Run genome background annotation</option>
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69 </param>
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70
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71 <when value="bed">
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72 <param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/>
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73 </when>
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74
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75 <when value="wig">
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76 <param format="wig" name="chip_wig" type="data" label="WIG file with ChiP enrichment signal"/>
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77 </when>
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78
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79 <when value="both1">
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80 <param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/>
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81 <param format="wig" name="chip_wig" type="data" label="WIG file with ChiP enrichment signal"/>
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82 </when>
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83
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84 <when value="both2">
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85 <param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/>
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86 <param format="wig" name="chip_wig" type="data" label="WIG file for genome background annotation"/>
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87 </when>
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88 </conditional>
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89
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90 <param name="refgene_table" label="Gene annotation table" type="select">
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91 <options from_data_table="ceas_refgene_tables">
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92 <filter type="sort_by" column="1"/>
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93 <validator type="no_options" message="No indexes are available for the selected dataset"/>
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94 </options>
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95 </param>
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96
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97 <param format="bed" name="extra_bed" type="data" optional="true" label="BED file of extra regions of interest (e.g. non-coding regions)"/>
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98
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99 <param name="sizes" type="integer" optional="true" label="Promoter (also downstream) sizes for ChIP region annotation" help="Three comma-separated integers or a single integer. Leave blank for default."/>
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100
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101 <param name="bisizes" type="integer" optional="true" label="Bidirectional promoter sizes for ChIP region annotation" help="Two comma-separated integers or a single integer. Leave blank for default."/>
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102
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103 <param name="span" type="integer" optional="true" label="Span from TSS and TTS in the gene-centered annotation" help="Leave blank for default."/>
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104 <param name="pfres" type="integer" optional="true" label="WIG profiling resolution" help="Leave blank for default."/>
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105 <param name="reldist" type="integer" optional="true" label="Relative distance to TSS/TTS in wig profiling" help="Leave blank for default."/>
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106
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107 </inputs>
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108
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109 <outputs>
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110 <data format="tabular" name="annot_out" label="Gene-centered annotation from ${tool.name} on ${on_string} (XLS)">
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111 <filter>(analysis_files['wig_or_bed'] != 'wig')</filter>
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112 </data>
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113 <data format="txt" name="r_out" label="R script for graph results from ${tool.name} on ${on_string}" />
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114 <data format="pdf" name="pdf_out" label="Graph results from ${tool.name} on ${on_string} (PDF)" />
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115 </outputs>
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116
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117 <help>
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118 Options:
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119 -b BED, --bed=BED BED file of ChIP regions.
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120 -w WIG, --wig=WIG WIG file for either wig profiling or genome background
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121 annotation. WARNING: --bg flag must be set for genome
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122 background re-annotation.
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123 -e EBED, --ebed=EBED BED file of extra regions of interest (eg, non-coding
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124 regions)
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125 -g GDB, --gt=GDB Gene annotation table (eg, a refGene table in sqlite3
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126 db format provided through the CEAS web,
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127 http://liulab.dfci.harvard.edu/CEAS/download.html).
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128 --sizes=SIZES Promoter (also dowsntream) sizes for ChIP region
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129 annotation. Comma-separated three values or a single
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130 value can be given. If a single value is given, it
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131 will be segmented into three equal fractions (ie, 3000
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132 is equivalent to 1000,2000,3000), DEFAULT:
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133 1000,2000,3000. WARNING: Values > 10000bp are
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134 automatically set to 10000bp.
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135 --bisizes=BISIZES Bidirectional-promoter sizes for ChIP region
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136 annotation Comma-separated two values or a single
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137 value can be given. If a single value is given, it
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138 will be segmented into two equal fractions (ie, 5000
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139 is equivalent to 2500,5000) DEFAULT: 2500,5000bp.
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140 WARNING: Values > 20000bp are automatically set to
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141 20000bp.
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142 --bg Run genome BG annotation again. WARNING: This flag is
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143 effective only if a WIG file is given through -w
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144 (--wig). Otherwise, ignored.
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145 --span=SPAN Span from TSS and TTS in the gene-centered annotation.
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146 ChIP regions within this range from TSS and TTS are
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147 considered when calculating the coverage rates in
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148 promoter and downstream, DEFAULT=3000bp
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149 --pf-res=PF_RES Wig profiling resolution, DEFAULT: 50bp. WARNING:
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150 Value smaller than the wig interval (resolution) may
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151 cause aliasing error.
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152 --rel-dist=REL_DIST Relative distance to TSS/TTS in wig profiling,
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153 DEFAULT: 3000bp
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154 </help>
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155
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156 </tool>
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