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annotate find_intervals.xml @ 21:d6b961721037

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Miller Lab Devshed version 4c04e35b18f6
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 05 Nov 2012 12:44:17 -0500
parents 8ae67e9fb6ff
children 95a05c1ef5d5
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1 <tool id="gd_find_intervals" name="Remarkable Intervals" version="1.0.0">
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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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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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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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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 not gd_snp.">
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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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63
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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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71
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72 <tests>
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73 <test>
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74 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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75 <param name="score_col" value="5" />
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76 <param name="type" value="value" />
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77 <param name="cutoff_val" value="700.0" />
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78 <param name="shuffles" value="10" />
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79 <param name="out_format" value="0" />
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80 <param name="choice" value="0" />
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81
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82 <output name="output" file="test_out/find_intervals/find_intervals.interval" />
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83 </test>
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84 </tests>
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85
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86 <help>
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87
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88 **Dataset formats**
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89
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90 The input dataset is tabular_, with required columns of chromosome, position,
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91 and score (in any column).
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92 The output dataset is interval_. (`Dataset missing?`_)
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93
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94 .. _interval: ./static/formatHelp.html#interval
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95 .. _tabular: ./static/formatHelp.html#tab
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96 .. _Dataset missing?: ./static/formatHelp.html
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97
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98 -----
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99
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100 **What it does**
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101
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102 The user selects a tabular dataset (such as a gd_snp dataset) and
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103 if the dataset is not also gd_snp format, specifies
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104 the columns containing chromosome, position, and scores (such as an Fst-value for the SNP).
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105 For gd_snp format the metadata can be used to specify the chromosome and
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106 position.
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107 Other inputs include
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108 a percentage or raw score for the "score-shift" which should be greater than the
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109 average value for the scores column. A higher value will give smaller intervals
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110 in the output.
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111 If a percentage (e.g. 95%) is specified
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112 then that percentile of the scores is used as the shift;
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113 percentile may not work well if many rows or SNPs have the same score
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114 (in that case use a raw score). The program subtracts the
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115 shift from every score, then finds genomic intervals (i.e., consecutive runs
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116 of SNPs) whose total score cannot be increased by adding or subtracting one
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117 or more adjusted scores at the ends of the interval.
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118 Another input is the number of times the
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119 data should be randomized (only intervals with score exceeding the maximum for
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120 the randomized data are reported).
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121 If 100 shuffles are requested, then any interval reported by the tool has a
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122 score with probability less than 0.01 of being equaled or exceeded by chance.
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123
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124 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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125
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
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126 **Example**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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127
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
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128 - input (gd_snp)::
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
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129
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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130 Contig222_chr2_9817738_9818143 220 C T 888.0 chr2 9817960 C 17 0 2 78 12 0 2 63 20 0 2 87 8 0 2 51 11 0 2 60 12 0 2 63 Y 76 0.093 1
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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131 Contig47_chr2_25470778_25471576 126 G A 888.0 chr2 25470896 G 12 0 2 63 14 0 2 69 14 0 2 69 10 0 2 57 18 0 2 81 13 0 2 66 N 11 0.289 1
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
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132 ...
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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133 Contig115_chr2_61631913_61632510 310 G T 999.3 chr2 61632216 G 7 0 2 48 9 0 2 54 7 0 2 48 11 0 2 60 10 0 2 57 10 0 2 57 N 13 0.184 0
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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134 Contig31_chr2_67331584_67331785 39 C T 999.0 chr2 67331623 C 11 0 2 60 10 0 2 57 7 0 2 48 9 0 2 54 2 0 2 33 4 0 2 39 N 110 0.647 1
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
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135 etc.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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136
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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137 - output not reporting individual positions::
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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138
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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139 chr2 9817960 67331624 1272.2000
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140
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
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141 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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142 </tool>