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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 --step $step
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16 --replicates $replicates
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17 --low_limit $low_limit
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18 --up_limit $up_limit
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19 --output_files $output_files_cond.output_files
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20 --output_summary "$output_summary"
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21 #if str($output_files_cond.output_files) in ["all", "simple_orphan"]:
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22 --output_orphan "$output_orphan"
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23 #end if
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24 #if str($output_files_cond.output_files) =="all":
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25 --plot_format $output_files_cond.plot_format
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26 --output_detail "$output_detail"
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27 --output_key "$output_key"
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28 --output_histogram "$output_histogram"
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29 #end if
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30 </command>
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31 <inputs>
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32 <param name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" />
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33 <param name="method" type="select" label="Method of finding match">
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34 <option value="closest" selected="True">Closest</option>
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35 <option value="largest">Largest</option>
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36 <option value="all">All</option>
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37 </param>
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38 <param name="distance" type="integer" value="50" min="0" label="Maximum distance between peaks in different replicates to allow merging" />
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39 <param name="step" type="integer" value="0" min="0" label="Step size" help="Distance for each iteration" />
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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 <param name="low_limit" type="integer" value="-1000" label="Lower limit for Crick-Watson distance filter" />
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42 <param name="up_limit" type="integer" value="1000" label="Upper limit for Crick-Watson distance filter" />
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43 <conditional name="output_files_cond">
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44 <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." >
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45 <option value="all" selected="True">no restrictions (output everything)</option>
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46 <option value="simple">matched pairs only</option>
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47 <option value="simple_orphan">matched pairs and orphans only</option>
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48 </param>
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49 <when value="simple" />
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50 <when value="simple_orphan" />
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51 <when value="all">
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52 <param name="plot_format" type="select" label="Output format for graph">
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53 <option value="pdf" selected="True">Pdf</option>
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54 <option value="png">Png</option>
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55 <option value="svg">Svg</option>
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56 </param>
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57 </when>
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58 </conditional>
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59 </inputs>
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60 <outputs>
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61 <data name="output_summary" format="gff" label="Matched pairs: ${tool.name} on ${on_string}" />
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62 <data name="output_orphan" format="tabular" label="Orphans: ${tool.name} on ${on_string}">
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63 <filter>output_files_cond["output_files"] in ["all", "simple_orphan"]</filter>
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64 </data>
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65 <data name="output_detail" format="tabular" label="Details: ${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_key" format="tabular" label="Key: ${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_histogram" format="pdf" label="Histogram: ${tool.name} on ${on_string}">
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72 <filter>output_files_cond["output_files"] == "all"</filter>
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73 <actions>
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74 <action type="format">
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75 <option type="from_param" name="output_files_cond.plot_format" />
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76 </action>
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77 </actions>
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78 </data>
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79 </outputs>
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80 <tests>
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81 <param name="input" value="closest_s_input1.gff" ftype="gff" />
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82 <param name="input" value="largest_s_input1.gff" ftype="gff" />
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83 <param name="method" value="closest" />
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84 <param name="distance" value="50" />
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85 <param name="step" value="0" />
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86 <param name="replicates" value="2" />
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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 <param name="output_files" value="all" />
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90 <param name="plot_format" value="png" />
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91 <output name="output_summary" file="summary_out1.gff" ftype="gff" />
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92 <output name="output_orphan" file="orphan_out1.tabular" ftype="tabular" />
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93 <output name="output_detail" file="orphan_detail1.tabular" ftype="tabular" />
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94 <output name="output_key" file="key_out1.tabular" ftype="tabular" />
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95 <output name="output_histogram" file="histogram_out1.pdf" ftype="pdf" compare="sim_size" />
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96 </tests>
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97 <help>
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98 **What it does**
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99 <![CDATA[
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100
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101 Replicate matching - matches paired peaks from two or more replicates and produces a list of matched
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102 groups and optionally a list of matched orphans. Additional optional outputs include the median read
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103 count for each input, details and a histogram.
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104
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105 ]]>
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106
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107 **Options**
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108
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109 * **Method** - Method to use when calling replicates.
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110 * **Distance** - Maximum distance between peaks in different replicates to allow merging.
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111 * **Step Size** - Distance for each iteration.
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112 * **Replicates** - Minimum number of replicates to call a peak. Number of replicates required must be at least 2.
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113 * **Lower Limit** - Lower limit for the Crick-Watson distance filter.
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114 * **Upper Limit** - Upper limit for the Crick-Watson distance filter.
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115 * **Plot Format** - Output format for graph. The options are PNG or SVG.
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116 </help>
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117 <expand macro="citations" />
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118 </tool>
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