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annotate idr.xml @ 0:d3ebbf39b1c5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
author iuc
date Tue, 22 Aug 2017 05:20:25 -0400
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d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
iuc
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1 <?xml version="1.0"?>
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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2 <tool id="idr" name="IDR" version="@VERSION@">
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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3 <description>compare ranked list of identifications</description>
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4 <macros>
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5 <token name="@VERSION@">2.0.3</token>
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">idr</requirement>
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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9 </requirements>
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10 <command detect_errors="aggressive">
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11 <![CDATA[
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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12 idr --samples '$primus' '$secundus'
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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13 #if $peak_list:
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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14 --peak-list '$peak_list'
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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15 #end if
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16 #if $input_file_type:
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17 #if $primus.dataset.ext == 'gff':
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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18 --input-file-type gff
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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19 #else:
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20 --input-file-type $input_file_type
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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21 #end if
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22 #end if
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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23 #if $idr_threshold:
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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24 --idr-threshold $idr_threshold
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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25 #end if
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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26 #if $rank != 'default':
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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27 --rank $rank
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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28 #end if
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29 --output-file idrValues.bed
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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30 --soft-idr-threshold $soft_idr_threshold
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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31 $plot $use_nonoverlapping_peaks --peak-merge-method $peak_merge_method
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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32 --initial-mu $initial_mu --initial-sigma $initial_sigma --initial-rho $initial_rho
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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33 --initial-mix-param $initial_mix_param $fix_mu $fix_sigma
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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34 $dont_filter_peaks_below_noise_mean $use_best_multisummit_idr
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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35 $allow_negative_scores --random-seed $random_seed --max-iter $max_iter
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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36 --convergence-eps $convergence_eps $only_merge_peaks
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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37 ]]>
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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38 </command>
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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39 <inputs>
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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40 <param name="primus" argument="--samples" type="data" format="bed,gff" label="First set of peaks in GFF or BED format" />
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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41 <param name="secundus" argument="--samples" type="data" format="bed,gff" label="Second set of peaks in GFF or BED format" />
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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42 <param name="peak_list" argument="--peak-list" type="data" format="bed,gff" optional="True" label="List of peaks to filter by" />
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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43 <param name="input_file_type" argument="--input-file-type" type="select" label="Input BED format" help="This option is ignored if the input file is GFF">
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44 <option value="" selected="true">Vanilla BED</option>
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45 <option value="gff">GFF</option>
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46 <option value="broadPeak">ENCODE broadPeak</option>
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47 <option value="narrowPeak">ENCODE narrowPeak</option>
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48 </param>
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49 <param argument="--rank" type="select" label="Column to use for ranking peaks">
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50 <option value="default">Use default</option>
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51 <option value="signal.value">signal</option>
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52 <option value="p.value">p value</option>
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53 <option value="q.value">q value</option>
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54 </param>
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55 <param name="idr_threshold" argument="--idr-threshold" type="float" optional="true" value="" />
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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56 <param name="soft_idr_threshold" argument="--soft-idr-threshold" type="float" value="0.05" />
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57 <param argument="--plot" type="boolean" truevalue="--plot" falsevalue="" label="Output PNG plot of peaks" />
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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58 <param name="use_nonoverlapping_peaks" argument="--use-nonoverlapping-peaks" type="boolean" truevalue="--use-nonoverlapping-peaks" falsevalue="" label="Use peaks without an overlapping match and set the value to 0" />
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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59 <param name="peak_merge_method" argument="--peak-merge-method" type="select" label="Method to use for merging peaks">
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60 <option value="sum">Sum</option>
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61 <option value="avg">Average</option>
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62 <option value="min">Min</option>
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63 <option value="max">Max</option>
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64 </param>
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65 <param name="initial_mu" argument="--initial-mu" type="float" value="0.1" label="Initial value of mu" />
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66 <param name="initial_sigma" argument="--initial-sigma" type="float" value="1.0" label="Initial value of sigma" />
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67 <param name="initial_rho" argument="--initial-rho" type="float" value="0.2" label="Initial value of rho" />
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68 <param name="initial_mix_param" argument="--initial-mix-param" type="float" value="0.5" label="Initial value of the mixture parameters" />
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69 <param name="fix_mu" argument="--fix-mu" type="boolean" truevalue="--fix-mu" falsevalue="" label="Fix mu to the starting point and do not let it vary" />
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70 <param name="fix_sigma" argument="--fix-sigma" type="boolean" truevalue="--fix-sigma" falsevalue="" label="Fix sigma to the starting point and do not let it vary" />
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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71 <param name="dont_filter_peaks_below_noise_mean" argument="--dont-filter-peaks-below-noise-mean" type="boolean" truevalue="--dont-filter-peaks-below-noise-mean" falsevalue="" label="Allow signal points that are below the noise mean" />
d3ebbf39b1c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 65024f2c106a2a7af0e2b656123058393941c41b
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72 <param name="use_best_multisummit_idr" argument="--use-best-multisummit-IDR" type="boolean" truevalue="--use-best-multisummit-IDR" falsevalue="" label="Set the IDR value for a group of multi summit peaks" help="A group of peaks with the same chr/start/stop but different summits" />
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73 <param name="allow_negative_scores" argument="--allow-negative-scores" type="boolean" truevalue="--allow-negative-scores" falsevalue="" label="Allow negative values for scores" />
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74 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="The random seed value" />
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75 <param name="max_iter" argument="--max-iter" type="integer" value="3000" label="The maximum number of optimization iterations" />
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76 <param name="convergence_eps" argument="--convergence-eps" type="float" value="0.000001" label="The maximum change in parameter value changes for convergence" />
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77 <param name="only_merge_peaks" argument="--only-merge-peaks" type="boolean" truevalue="--only-merge-peaks" falsevalue="" label="Only return the merged peak list" />
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78 </inputs>
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79 <outputs>
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80 <data format="bed" name="idr_values" from_work_dir="idrValues.bed" label="${tool.name} on ${on_string}: IDR Values">
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81 <actions>
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82 <action type="format">
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83 <option type="from_param" name="primus" param_attribute="ext" />
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84 </action>
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85 </actions>
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86 </data>
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87 <data format="png" name="idr_plot" from_work_dir="idrValues.bed.png" label="${tool.name} on ${on_string}: PNG Plot">
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88 <filter>plot</filter>
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89 </data>
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="primus" value="idr_input1.1.bed" ftype="bed" />
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94 <param name="secundus" value="idr_input1.2.bed" ftype="bed" />
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95 <param name="rank" value="default" />
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96 <param name="plot" value="True" />
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97 <output name="idr_values" file="idr_out1.bed" ftype="bed" />
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98 <output name="idr_plot" file="idr_out1.png" ftype="png" />
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99 </test>
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100 <test>
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101 <param name="primus" value="idr_input2.1.bed" ftype="bed" />
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102 <param name="secundus" value="idr_input2.2.bed" ftype="bed" />
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103 <param name="rank" value="default" />
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104 <param name="plot" value="True" />
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105 <output name="idr_values" file="idr_out2.bed" ftype="bed" />
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106 <output name="idr_plot" file="idr_out2.png" ftype="png" />
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107 </test>
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108 <test>
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109 <param name="primus" value="idr_input3.1.bed" ftype="bed" />
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110 <param name="secundus" value="idr_input3.2.bed" ftype="bed" />
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111 <param name="peak_list" value="idr_input3.3.bed" ftype="bed" />
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112 <param name="rank" value="default" />
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113 <param name="plot" value="True" />
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114 <output name="idr_values" file="idr_out3.bed" ftype="bed" />
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115 <output name="idr_plot" file="idr_out3.png" ftype="png" />
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116 </test>
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117 <test>
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118 <param name="primus" value="idr_input4.1.gff" ftype="gff" />
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119 <param name="secundus" value="idr_input4.2.gff" ftype="gff" />
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120 <param name="input_file_type" value="gff" />
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121 <param name="rank" value="default" />
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122 <param name="plot" value="True" />
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123 <output name="idr_values" file="idr_out4.gff" ftype="gff" />
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124 <output name="idr_plot" file="idr_out4.png" ftype="png" />
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125 </test>
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126 </tests>
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127 <help>
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128 <![CDATA[
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129 The `IDR <https://github.com/nboley/idr/blob/master/README.md>`__ (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. Unlike the usual scalar measures of reproducibility, the IDR approach creates a curve, which quantitatively assesses when the findings are no longer consistent across replicates.
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130 ]]>
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131 </help>
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132 <citations>
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133 <citation type="doi">10.1214/11-AOAS466</citation>
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134 </citations>
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135 </tool>