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1 <tool id ="pyCalculateFDRs" name="pyCalculateFDRs">
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2 <requirements>
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3 <requirement type="package">pyCRAC</requirement>
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4 </requirements>
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5 <command interpreter="python">
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6 /usr/local/bin/pyCalculateFDRs.py
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7 -f $ftype.input
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8 --file_type $ftype.file_type
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9 --gtf=$addGTF.gtf
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10
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11 #if $addGTF.annotate.annotations != "all":
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12 #if $addGTF.gtfFile == "default" and $addGTF.annotate.annotations == "auto":
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13 --annotation $addGTF.annotate.scan.annotation
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14 #else:
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15 --annotation $addGTF.annotate.annotation
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16 #end if#
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17 #end if#
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18 --chromfile=$addChr.chr
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19 #if $addOpt.options == "edit"
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20 -s $addOpt.sequence
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21 --min $addOpt.min
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22 --minfdr $addOpt.minfdr
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23 --iterations=$addOpt.iterations
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24 --range $addOpt.range
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25 #end if#
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26 -o $output
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27
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28 </command>
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29 <version_command>/usr/local/bin/pyCalculateFDRs.py --version</version_command>
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30 <inputs>
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31 <conditional name="ftype">
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32 <param name="file_type" type="select" label="Input File Type --file_type" help="Use bed6, gff or gtf input files containing read/cDNA co-ordinates">
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33 <option value="gff" selected="true">GFF</option>
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34 <option value="bed">Bed6</option>
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35 <option value="gtf">GTF</option>
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36 </param>
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37 <when value="gff">
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38 <param format="gff" name="input" type="data" label="Input File --readdatafile" help="GFF format containing read/cDNA co-ordinates" />
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39 </when>
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40 <when value="gtf">
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41 <param format="gtf" name="input" type="data" label="Input File --readdatafile" help="GTF format containing read/cDNA co-ordinates" />
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42 </when>
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43 <when value="bed">
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44 <param format="bed6" name="input" type="data" label="Input File --readdatafile" help="Bed 6 column format containing read/cDNA co-ordinates" />
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45 </when>
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46 </conditional>
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47
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48 <conditional name="addChr">
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49 <param name="chrfile" type="select" label="Choose Chromosome length file from">
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50 <option value="default" selected="true">Defaults</option>
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51 <option value="other">History</option>
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52 </param>
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53 <when value="default">
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54 <param name="chr" type="select" label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes">
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55 <options from_data_table="pycrac_chr"/>
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56 </param>
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57 </when>
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58 <when value="other">
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59 <param format="tabular" name="chr" type="data" label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes. Use pyCrac utility pyCalculateChromosomeLengths to create."/>
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60 </when>
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61 </conditional>
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62
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63 <conditional name="addGTF">
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64 <param name="gtfFile" type="select" label="Choose GTF File from">
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65 <option value="default" selected="true">Defaults</option>
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66 <option value="other">History</option>
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67 </param>
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68 <when value="default">
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69 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
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70 <options from_data_table="pycrac_gtf"/>
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71 </param>
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72 <conditional name="annotate">
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73 <param name="annotations" type="select" label="Select annotation">
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74 <option value="all" selected="true">All</option>
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75 <option value="manual">Enter in text box</option>
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76 <option value="auto">Scan pyGetGTFSources file</option>
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77 </param>
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78 <when value="all">
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79 <param name="annotation" type="hidden" format="txt" size="10" value="all"/>
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80 </when>
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81 <when value="manual">
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82 <param name="annotation" type="text" format="txt" size="100" value="protein_coding" label="Select which annotation to focus search on --annotation" help="To find a list of available annotations please use pyGetGTFSources tool">
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83 <validator type="empty_field" message="Please enter a value"/>
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84 </param>
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85 </when>
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86 <when value="auto">
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87 <param format="tabular" name="gtf_annotation" type="data" label="GTF annotation File (pyGetGTFSources output)" help="Tabular file containing unique list of annotations/sources in selected GTF file. Refer to pyGetGTFSources"/>
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88 <conditional name="scan">
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89 <param name="annotations" type="select" label="Scan this file for annotations" help="Choose the correct GTF file then choose GO">
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90 <option value="wait" selected="true">Waiting</option>
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91 <option value="scanning">Go</option>
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92 </param>
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93 <when value="wait">
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94 </when>
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95 <when value="scanning">
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96 <param name="annotation" type="select" multiple="false" label="Select which annotation to focus search on --annotation">
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97 <options from_dataset="gtf_annotation">
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98 <column name="name" index="0"/>
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99 <column name="value" index="0"/>
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100 </options>
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101 </param>
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102 </when>
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103 </conditional>
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104 </when>
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105 </conditional>
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106 </when>
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107 <when value="other">
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108 <param format="gtf" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
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109 <conditional name="annotate">
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110 <param name="annotations" type="select" label="Select annotation">
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111 <option value="all" selected="true">All</option>
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112 <option value="manual">Enter in text box</option>
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113 <option value="auto">Scan selected file</option>
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114 </param>
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115 <when value="all">
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116 <param name="annotation" type="hidden" format="txt" size="10" value="all"/>
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117 </when>
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118 <when value="manual">
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119 <param name="annotation" type="text" format="txt" size="100" value="protein_coding" label="Select which annotation to focus search on --annotation" help="To find a list of available annotations please use pyGetGTFSources tool">
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120 <validator type="empty_field" message="Please enter a value"/>
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121 </param>
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122 </when>
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123 <when value="auto">
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124 <param name="annotation" type="select" multiple="false" label="Select which annotation to focus search on --annotation">
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125 <options from_dataset="gtf">
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126 <column name="name" index="1"/>
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127 <column name="value" index="1"/>
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128 <filter type="unique_value" name="unique" column="1"/>
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129 </options>
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130 </param>
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131 </when>
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132 </conditional>
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133 </when>
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134 </conditional>
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135 <conditional name="addOpt">
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136 <param name="options" type="select" label="Standard options">
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137 <option value="default" selected="true">Default</option>
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138 <option value="edit">Edit</option>
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139 </param>
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140 <when value="edit">
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141 <param name="sequence" type="select" label="Align reads to --sequence">
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142 <option value="genomic" selected="true">Genomic Sequence</option>
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143 <option value="coding">Coding Sequence</option>
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144 </param>
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145 <param format="integer" name="min" type="integer" label="Minimum read coverage --min " value="1" size="10" help="Set the minimal read coverage for a region">
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146 <validator type="in_range" min="1" message="Please enter a value >= 1"/>
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147 </param>
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148 <param name="minfdr" type="float" label="Minimum FDR threshold --minfdr" value="0.05" size="6" help="Set a minimal FDR threshold for filtering interval data">
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149 <validator type="in_range" min="0" max="1" message="Please enter a value between 0 and 1"/>
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150 </param>
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151 <param format="integer" name="iterations" type="integer" label="Number of iterations --iterations" value="100" size="6" help="The number of iterations for randomization of read coordinates">
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152 <validator type="in_range" min="0" message="Please enter a value >= 0"/>
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153 </param>
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154 <param format="integer" name="range" type="integer" label="Range --range" value="0" size="5" help="Manually set the length of the 5' and 3' UTRs 0>50000">
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155 <validator type="in_range" min="0" max="50000" message="Please enter a value between 0 and 50000"/>
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156 </param>
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157 </when>
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158 <when value="default">
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159 </when>
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160 </conditional>
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161 <param name="label" type="text" format="txt" size="30" value="pyCalculateFDRs" label="Enter output file label -o" />
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162 </inputs>
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163 <outputs>
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164 <data format="gtf" name="output" label="${label.value}.gtf"/>
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165 </outputs>
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166 <help>
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167
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168 .. class:: infomark
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169
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170 **pyCalculateFDRs**
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171
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172 By default the FDR value is set to 0.05, meaning that there is a 5% chance that the interval is not significantly enriched.
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173 The tool reports significant intervals in the GTF format and reports overlapping genomic features.
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174 Mutation frequencies are not included but these can be added using the pyCalculateMutationFrequencies tool
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175
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176 **NOTE!** By default it calls each significant interval an "exon" but this has no meaning! It may overlap with an intron.
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177 Use bedtools to extract those intervals that overlap with introns or other features
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178
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179 Example of an output file::
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180
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181 ##gff-version 2
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182 # generated by pyCalculateFDRs version 0.0.3, Sat Jun 1 21:16:23 2013
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183 # pyCalculateFDRs.py -f test_count_output_reads.gtf -r 200 -o test_count_output_FDRs_005.gtf -v -m 0.05
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184 # chromosome feature source start end minimal_coverage strand . attributes
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185 chrI protein_coding exon 140846 140860 5 - . gene_id "YAL005C"; gene_name "SSA1";
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186 chrI intergenic_region exon 223118 223164 4 - . gene_id "INT_0_179"; gene_name "INT_0_179";
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187 chrI intergenic_region exon 71889 71922 3 + . gene_id "INT_0_94"; gene_name "INT_0_94";
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188 chrII intergenic_region exon 296127 296158 3 - . gene_id "INT_0_365"; gene_name "INT_0_365";
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189 chrII intergenic_region exon 680697 680722 4 - . gene_id "INT_0_626"; gene_name "INT_0_626";
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190 chrII intergenic_region exon 680827 680846 4 - . gene_id "INT_0_626"; gene_name "INT_0_626";
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191 chrII snRNA exon 680827 680838 5 - . gene_id "LSR1"; gene_name "LSR1";
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192 chrII snRNA exon 680951 681001 5 - . gene_id "LSR1"; gene_name "LSR1";
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193 chrII intergenic_region exon 577985 577996 3 - . gene_id "INT_0_556"; gene_name "INT_0_556";
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194 chrII protein_coding exon 203838 203887 3 + . gene_id "YBL011W"; gene_name "SCT1";
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195 chrII protein_coding exon 296127 296158 3 - . gene_id "YBR028C"; gene_name "YBR028C";
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196
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197
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198 pyCalculateFDRs is part of the pyCRAC_ package. Takes interval information in GTF or bed format and calculates False Discovery Rates (FDRs).
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199
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200
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201 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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202
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203 ------
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204
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205 **Parameter list**
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206
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207 Options::
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208
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209 -f read_file, --readdatafile=read_file
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210 Name of the bed/gff/gtf file containing the read/cDNA
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211 coordinates
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212 --file_type=FILE_TYPE
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213 this tool supports bed6, gtf and gff input files.
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214 Please select from 'bed','gtf' or 'gff'. Default=gtf
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215 -o outfile.gtf, --outfile=outfile.gtf
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216 Optional. Provide the name of the output file. Default
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217 is 'selected_intervals.gtf'
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218 -r 100, --range=100
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219 allows you to set the length of the UTR regions. If
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220 you set '-r 50' or '--range=50', then the program will
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221 set a fixed length (50 bp) regardless of whether the
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222 GTF file has genes with annotated UTRs.
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223 -a protein_coding, --annotation=protein_coding
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224 select which annotation (i.e. protein_coding, ncRNA,
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225 sRNA, rRNA,snoRNA,snRNA, depending on the source of
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226 your GTF file) you would like to focus your analysis
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227 on. Default = all annotations
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228 -c yeast.txt, --chromfile=yeast.txt
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229 Location of the chromosome info file. This file should
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230 have two columns: first column is the names of the
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231 chromosomes, second column is length of the
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232 chromosomes. Default is yeast
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233 --gtf=yeast.gtf
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234 Name of the annotation file. Default is /usr/local/pyC
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235 RAC/db/Saccharomyces_cerevisiae.EF2.59.1.2.gtf
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236 -m MINFDR, --minfdr=MINFDR
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237 To set a minimal FDR threshold for filtering interval
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238 data. Default is 0.05
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239 --min=MIN
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240 to set a minimal read coverages for a region. Regions
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241 with coverage less than minimum will be ignoredve an
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242 FDR of zero
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243 --iterations=ITERATIONS
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244 to set the number of iterations for randomization of
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245 read coordinates. Default=100
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246 </help>
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247 </tool>
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