Mercurial > repos > iuc > repmatch_gff3

annotate repmatch_gff3.xml @ 1:e5c7fffdc078 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
author iuc
date Tue, 26 Jul 2016 06:10:53 -0400
parents a072f0f30ea3
children d7f1312b3455
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a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
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1 <?xml version="1.0"?>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
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2 <tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.0">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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3 <description>Match paired peaks from two or more replicates</description>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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4 <macros>
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iuc
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5 <import>repmatch_gff3_macros.xml</import>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 python $__tool_directory__/repmatch_gff3.py
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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10 #for $i in $input:
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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11 --input "${i}" "${i.hid}"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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12 #end for
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13 --method $method
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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14 --distance $distance
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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15 --replicates $replicates
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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16 --output_files $output_files_cond.output_files
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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17 --output_matched_peaks "$output_matched_peaks"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
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18 #if str($output_files_cond.output_files) in ["all", "matched_peaks_unmatched_peaks"]:
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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19 --output_unmatched_peaks "$output_unmatched_peaks"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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20 #end if
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21 #if str($output_files_cond.output_files) =="all":
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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22 --output_detail "$output_detail"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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23 --output_statistics_table "$output_statistics_table"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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24 --output_statistics_histogram "$output_statistics_histogram"
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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25 #end if
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26 #if str($advanced_options_cond.advanced_options) == "on":
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27 --step $advanced_options_cond.step
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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28 --low_limit $advanced_options_cond.low_limit
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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29 --up_limit $advanced_options_cond.up_limit
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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30 #end if
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31 </command>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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32 <inputs>
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33 <param name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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34 <param name="method" type="select" label="Method of finding match">
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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35 <option value="closest" selected="True">Closest</option>
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36 <option value="largest">Largest</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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37 <option value="all">All</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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38 </param>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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39 <param name="distance" type="integer" value="50" min="0" label="Maximum distance between peaks in different replicates to allow merging" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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40 <param name="replicates" type="integer" value="2" min="2" label="Minimum number of replicates that must be matched for merging to occur" />
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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41 <conditional name="output_files_cond">
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42 <param name="output_files" type="select" label="Select output" help="Statistics will always be generated." >
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43 <option value="all" selected="True">everything</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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44 <option value="matched_peaks">matched paired peaks only</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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45 <option value="matched_peaks_unmatched_peaks">matched paired peaks and unmatched paired peaks only</option>
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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46 </param>
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47 <when value="matched_peaks" />
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48 <when value="matched_peaks_unmatched_peaks" />
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49 <when value="all" />
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50 </conditional>
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51 <conditional name="advanced_options_cond">
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52 <param name="advanced_options" type="select" label="Advanced options">
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53 <option value="off" selected="true">Hide advanced options</option>
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54 <option value="on">Display advanced options</option>
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55 </param>
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56 <when value="on">
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57 <param name="step" type="integer" value="0" min="0" label="Step size" help="Distance for each iteration" />
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58 <param name="low_limit" type="integer" value="-1000" label="Lower limit for Crick-Watson distance filter" />
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59 <param name="up_limit" type="integer" value="1000" label="Upper limit for Crick-Watson distance filter" />
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60 </when>
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61 <when value="off" />
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62 </conditional>
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63 </inputs>
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64 <outputs>
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65 <data name="output_statistics_table" format="tabular" label="Statistics Table: ${tool.name} on ${on_string}">
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66 <filter>output_files_cond["output_files"] == "all"</filter>
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67 </data>
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68 <data name="output_statistics_histogram" format="pdf" label="Statistics Histogram: ${tool.name} on ${on_string}">
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69 <filter>output_files_cond["output_files"] == "all"</filter>
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70 </data>
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71 <data name="output_detail" format="tabular" label="Data D: ${tool.name} on ${on_string}">
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72 <filter>output_files_cond["output_files"] == "all"</filter>
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73 </data>
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74 <data name="output_unmatched_peaks" format="tabular" label="Data UP: ${tool.name} on ${on_string}">
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75 <filter>output_files_cond["output_files"] in ["all", "matched_peaks_unmatched_peaks"]</filter>
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76 </data>
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77 <data name="output_matched_peaks" format="gff" label="Data MP: ${tool.name} on ${on_string}" />
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78 </outputs>
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79 <tests>
1
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80 <test>
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81 <param name="input" value="closest_matched_pairs_input1.gff,largest_matched_pairs_input1.gff" ftype="gff" />
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82 <param name="method" value="closest" />
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83 <param name="distance" value="50" />
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84 <param name="replicates" value="2" />
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85 <param name="output_files" value="all" />
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86 <param name="step" value="0" />
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87 <param name="low_limit" value="-1000" />
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88 <param name="up_limit" value="1000" />
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89 <output name="output_statistics_table" file="statistics_table_out1.tabular" ftype="tabular" />
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90 <output name="output_statistics_histogram" file="magic.pdf" ftype="pdf" compare="contains" />
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91 <output name="output_detail" file="detail_out1.tabular" ftype="tabular" />
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92 <output name="output_unmatched_peaks" file="unmatched_peaks_out1.tabular" ftype="tabular" />
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93 <output name="output_matched_peaks" file="matched_peaks_out1.gff" ftype="gff" />
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94 </test>
0
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95 </tests>
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96 <help>
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97 **What it does**
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98
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99 RepMatch accepts two or more input datasets, and starts by defining peak-pair midpoints in the first dataset. It then
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100 discovers all peak-pair midpoints in the second dataset that are within the distance, defined by the tool's **Maximum
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101 distance between peaks in different replicates to allow merging** parameter, from the peak-pair midpoint coordinate in
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102 the first dataset. When encountering multiple candidates to match (one-to-many), RepMatch uses the method defined by
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103 the tool's **Method of finding match** parameter so that there is at most only a one-to-one match across the two datasets.
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104 This method provides the following options:
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105
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106 * **closest** - matches only the closest one in bp distance.
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107 * **largest** - matches the one that contain the most number of reads.
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108 * **all** - both methods are run separately.
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109
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110 RepMatch matching is an iterative process, as it attempts to find the centroid coordinate amongst all replicates. As such,
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111 the centroid is the point of reference for "distqnce" and "closest". This process can be sped up by increasing the tool's
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112 **Step size** parameter.
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113
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114 The minimum number of replicates that can be matched for a match to occur is defined by the tool's **Minimum number of
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115 replicates that must be matched for merging to occur** parameter. Additional filters can be applied using the tool's
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116 **Advanced options**, including a lower and upper limit for the C-W distance.
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117
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118 .. image:: $PATH_TO_IMAGES/repmatch.png
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119
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120 -----
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121
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122 **Options**
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123
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124 * **Distance** - Maximum distance for discovering all peak-pair midpoints in a second dataset relative to the peak-pair midpoints in the first dataset
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125 * **Method** - Method to use when encountering multiple candidates to match so that there is at most only a one-to-one match across the two datasets.
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126 * **Step Size** - Distance for each iteration.
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127 * **Replicates** - Minimum number of replicates that can be matched for a match to occur. This value must be at least 2.
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128 * **Lower Limit** - Lower limit for the Crick-Watson distance filter.
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129 * **Upper Limit** - Upper limit for the Crick-Watson distance filter.
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130
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131 -----
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132
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133 **Output Data Files**
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134
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135 * **Data MP** - gff file consisting of only peak pairs
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136
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137 - Columns are **chr**, **script**, **blank**, **peak start**, **peak end**, **blank**, **normalized tag counts**, **blank** and **info**.
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138 - Peak start and end are separated by one coordinate.
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139 - Normalized tag is the occupancy averaged across replicates.
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140 - Attributes include C-W distance, sum total of tag counts, number of replicates merged.
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141
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142 * **Data D** - tabular file consisting of the list of all matched replicates.
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143 * **Data UP** - tabular file consisting of all unmatched peak-pairs.
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144
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145 **Output Statistics Files**
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146
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147 * **Statistics Table** - tabular file providing the description key of **Data D**.
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148 * **Statistics Histogram** - graph of the number of matched locations having the indicated replicate counts.
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149
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150 **Comments on Replicates**
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151
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152 Three types of replicates may be considered. Biological replicates represent independently collected biological samples.
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153 At least two biological replicate must be performed for each experiment from which a conclusion is being drawn, and the
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154 conclusion must be evident in both biological replicates when analyzed separately. Technical replicates represent a re-run
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155 of the assay on the same biological material. This is usually done when one replicate fails to produce quality data, and is
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156 used to replace that earlier replicate. Sequencing replicates represent additional sequencing of the same successful library
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157 in order to obtain more reads should the analysis require it. The reads from individual sequencing replicates are usually
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158 merged without need for separate analysis.
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159
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160 </help>
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161 <expand macro="citations" />
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162 </tool>