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annotate find_intervals.xml @ 38:9d0b1fa77047

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Changed simplejson to json
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 28 Feb 2014 12:15:32 -0500
parents a631c2f6d913
children
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1 <tool id="gd_find_intervals" name="Remarkable Intervals" version="1.1.0">
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2 <description>: Find high-scoring runs of SNPs</description>
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3
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4 <command interpreter="python">
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5 find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.files_path"
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6
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7 #if $override_metadata.choice == "0"
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8 "$input.metadata.ref" "$input.metadata.rPos"
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9 #else
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10 "$override_metadata.ref_col" "$override_metadata.rpos_col"
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11 #end if
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12
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13 "$score_col" "$shuffles"
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14
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15 #if $cutoff.type == 'percentage'
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16 "$cutoff.cutoff_pct"
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17 #else
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18 "=$cutoff.cutoff_val"
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19 #end if
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20
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21 "$out_format"
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22 </command>
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23
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24 <inputs>
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25 <param name="input" type="data" format="tabular" label="Dataset">
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26 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
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27 </param>
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28
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29 <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Column with score"/>
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30
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31 <conditional name="cutoff">
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32 <param name="type" type="select" label="Score-shift type">
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33 <option value="percentage">percentage</option>
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34 <option value="value">value</option>
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35 </param>
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36 <when value="percentage">
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37 <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage score-shift"/>
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38 </when>
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39 <when value="value">
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40 <param name="cutoff_val" type="float" value="0.0" label="Value score-shift"/>
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41 </when>
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42 </conditional>
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43
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44 <param name="shuffles" type="integer" min="0" value="0" label="Number of randomizations"/>
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45
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46 <param name="out_format" type="select" format="integer" label="Report individual positions">
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47 <option value="0" selected="true">no</option>
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48 <option value="1">yes</option>
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49 </param>
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50
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51 <conditional name="override_metadata">
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52 <param name="choice" type="select" format="integer" label="Choose columns" help="Note: you must choose the columns if the input dataset is neither gd_snp nor gd_genotype.">
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53 <option value="0" selected="true">no, get columns from metadata</option>
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54 <option value="1" >yes, choose columns here</option>
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55 </param>
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56 <when value="0" />
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57 <when value="1">
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58 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome" help="Note: be sure this corresponds to the build recorded in the metadata."/>
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59 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position" help="Note: either zero-based or one-based positions will work."/>
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60 </when>
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61 </conditional>
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62 </inputs>
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64 <outputs>
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65 <data name="output" format="interval">
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66 <change_format>
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67 <when input="out_format" value="1" format="bigwigpos" />
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68 </change_format>
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69 </data>
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70 </outputs>
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72 <requirements>
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73 <requirement type="package" version="0.1">gd_c_tools</requirement>
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74 </requirements>
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75
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76 <tests>
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77 <test>
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78 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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79 <param name="score_col" value="5" />
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80 <param name="type" value="value" />
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81 <param name="cutoff_val" value="700.0" />
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82 <param name="shuffles" value="10" />
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83 <param name="out_format" value="0" />
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84 <param name="choice" value="0" />
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85
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86 <output name="output" file="test_out/find_intervals/find_intervals.interval" />
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87 </test>
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88 </tests>
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89
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90 <help>
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91 **Dataset formats**
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92
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93 The input dataset is tabular_ (which includes gd_snp_ and gd_genotype_),
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94 with required columns of chromosome, position, and score (in any column).
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95 The output dataset is interval_. (`Dataset missing?`_)
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96
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97 .. _tabular: ./static/formatHelp.html#tab
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98 .. _gd_snp: ./static/formatHelp.html#gd_snp
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99 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
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100 .. _interval: ./static/formatHelp.html#interval
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101 .. _Dataset missing?: ./static/formatHelp.html
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102
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103 -----
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104
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105 **What it does**
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106
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107 The user selects a tabular dataset (such as the SNV formats gd_snp and
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108 gd_genotype) and if the dataset is not in an SNV format, specifies the
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109 columns containing chromosome, position, and scores (such as an FST-value
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110 for the SNP). With SNV formats, the metadata tells which columns hold the
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111 chromosome and position. Other inputs include a percentage or raw score
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112 for the "score-shift" which should be greater than the average value
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113 for the scores column. A higher value will give smaller intervals in
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114 the output. If a percentage (e.g. 95%) is specified then that percentile
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115 of the scores is used as the shift; percentile may not work well if many
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116 rows or SNPs have the same score (in that case use a raw score).
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117
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118 The program subtracts the shift from every score, then finds genomic
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119 intervals (i.e., consecutive runs of SNPs) whose total score cannot be
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120 increased by adding or subtracting one or more adjusted scores at the
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121 ends of the interval. Another input is the number of times the data
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122 should be randomized (only intervals with score exceeding the maximum
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123 for the randomized data are reported). If 100 shuffles are requested,
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124 then any interval reported by the tool has a score with probability
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125 less than 0.01 of being equaled or exceeded by chance, assuming that
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126 the scores vary independently by position.
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127
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128 -----
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129
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130 **Example**
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131
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132 - Input (showing only the chromosome, position, and score columns)::
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133
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134 chr2 39 0.40
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135 chr2 103 0.97
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136 chr2 188 0.72
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137 chr2 203 0.68
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138 chr2 321 0.92
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139 ...
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140 chr2 1132 0.85
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141 chr2 1321 0.34
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142 ...
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143
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144 - Suppose the user-specified score-shift is 0.75. This value is subtracted from each score, giving::
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145
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146 chr2 39 -0.35
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147 chr2 103 0.22
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148 chr2 188 -0.03
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149 chr2 203 -0.07
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150 chr2 321 0.17
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151 ...
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152 chr2 1132 0.10
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153 chr2 1321 -0.41
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154 ...
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155
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156 - The output, not reporting individual positions, might be (depending on the values not shown above)::
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157
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158 chr2 103 1132 1.42
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159 </help>
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160 </tool>
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161
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162