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1 <?xml version="1.0"?>
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2 <tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.0">
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3 <description>Match paired peaks from two or more replicates</description>
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4 <macros>
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5 <import>repmatch_gff3_macros.xml</import>
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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
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10 #for $i in $input:
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11 --input "${i}" "${i.hid}"
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12 #end for
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13 --method $method
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14 --distance $distance
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15 --replicates $replicates
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16 --output_files $output_files_cond.output_files
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17 --output_matched_peaks "$output_matched_peaks"
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18 #if str($output_files_cond.output_files) in ["all", "matched_peaks_unmatched_peaks"]:
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19 --output_unmatched_peaks "$output_unmatched_peaks"
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20 #end if
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21 #if str($output_files_cond.output_files) =="all":
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22 --output_detail "$output_detail"
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23 --output_statistics_table "$output_statistics_table"
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24 --output_statistics_histogram "$output_statistics_histogram"
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25 #end if
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11
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26 #if str($advanced_options_cond.advanced_options) == "on":
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27 --step $advanced_options_cond.step
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28 --low_limit $advanced_options_cond.low_limit
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29 --up_limit $advanced_options_cond.up_limit
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30 #end if
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31 </command>
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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" />
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34 <param name="method" type="select" label="Method of finding match">
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35 <option value="closest" selected="True">Closest</option>
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36 <option value="largest">Largest</option>
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37 <option value="all">All</option>
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38 </param>
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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" />
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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" />
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41 <conditional name="output_files_cond">
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42 <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." >
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43 <option value="all" selected="True">no restrictions (output everything)</option>
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44 <option value="matched_peaks">matched paired peaks only</option>
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45 <option value="matched_peaks_unmatched_peaks">matched paired peaks and unmatched paired peaks only</option>
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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>
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80 <param name="input" value="closest_matched_pairs_input1.gff" ftype="gff" />
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81 <param name="input" value="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="statistics_histogram_out1.pdf" ftype="pdf" compare="sim_size" />
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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 </tests>
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95 <help>
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96 **What it does**
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97
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98 Replicate matching - inspects paired peaks from two or more replicates and produces a list of matched
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99 paired peaks and optionally a list of unmatched paired peaks. Additional optional outputs include the
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100 median read count for each input, details and a histogram.
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101
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102 -----
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103
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104 **Options**
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105
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106 * **Distance** - Maximum distance between peaks in different replicates to allow merging.
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107 * **Method** - Method to use when calling replicates.
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108 * **Step Size** - Distance for each iteration.
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109 * **Replicates** - Minimum number of replicates to call a peak. Number of replicates required must be at least 2.
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110 * **Lower Limit** - Lower limit for the Crick-Watson distance filter.
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111 * **Upper Limit** - Upper limit for the Crick-Watson distance filter.
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112
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113 </help>
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114 <expand macro="citations" />
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115 </tool>
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