annotate makeWindowsBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
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1
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1 <tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 bedtools makewindows
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11 #if $type.type_select == 'genome':
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12 -g $type.genome
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13 #else:
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14 -b $type.input
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15 #end if
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16 #if $action.action_select == 'windowsize':
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17 -w $action.windowsize
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18 #if $action.step_size.step_size_select == 'yes':
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19 -s $action.step_size.step_size
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20 #end if
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21 #else:
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22 -n $action.number
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23 -s $action.step_size
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24 #end if
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25 $sourcename
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26 > $output
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27 ]]>
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28 </command>
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29 <inputs>
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30 <conditional name="type">
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31 <param name="type_select" type="select" label="Work with">
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32 <option value="bed" selected="True">Bed File</option>
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33 <option value="genome">Genome File</option>
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34 </param>
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35 <when value="bed">
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36 <param name="input" format="bed,vcf,gff,gff3" type="data" label="BED/VCF/GFF file"/>
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37 </when>
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38 <when value="genome">
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39 <expand macro="genome" />
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40 </when>
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41 </conditional>
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42 <conditional name="action">
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43 <param name="action_select" type="select" label="Work with">
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44 <option value="windowsize" selected="True">Set WindowSize</option>
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45 <option value="number">Give Number of Windows</option>
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46 </param>
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47 <when value="windowsize">
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48 <param name="windowsize" type="integer" value="1"
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49 label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
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50 help="i.e. same number of nucleotide in each window" />
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51 <conditional name="step_size">
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52 <param name="step_size_select" type="select"
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53 label="Specify Step size? i.e. how many base pairs to step before creating a new window"
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54 help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
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55 <option value="yes">Yes</option>
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56 <option value="no" selected="True">No</option>
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57 </param>
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58 <when value="yes">
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59 <param name="step_size" type="integer" value="100" label="Specify it" />
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60 </when>
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61 <when value="no" />
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62 </conditional>
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63 </when>
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64 <when value="number">
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65 <param name="number" type="integer" value="1"
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66 label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows"
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67 help="i.e. same number of windows, with varying window sizes" />
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68 <param name="step_size" type="integer" value="100" label="Specify it" />
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69 </when>
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70 </conditional>
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71 <param name="sourcename" type="select" label="ID Naming Options">
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72 <option value="" selected="True">Default</option>
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73 <option value="-i src">use the source interval's name</option>
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74 <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
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75 <option value="-i srcwinnum">use the source interval's name with the window number.</option>
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76 </param>
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77 </inputs>
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78 <outputs>
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79 <data name="output" format="bed" />
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="type_select" value="genome" />
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84 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
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85 <param name="action_select" value="windowsize" />
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86 <param name="windowsize" value="1000000" />
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87 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
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88 </test>
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89 <test>
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90 <param name="type_select" value="genome" />
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91 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
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92 <param name="action_select" value="windowsize" />
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93 <param name="windowsize" value="1000000" />
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94 <param name="step_size_select" value="yes" />
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95 <param name="step_size" value="50000" />
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96 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
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97 </test>
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98 <test>
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99 <param name="type_select" value="genome" />
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100 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
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101 <param name="action_select" value="number" />
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102 <param name="number" value="100" />
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103 <param name="step_size" value="10000" />
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104 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
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105 </test>
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106 <test>
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107 <param name="type_select" value="bed" />
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108 <param name="input" value="makeWindowBed1.bed" ftype="bed" />
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109 <param name="action_select" value="number" />
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110 <param name="number" value="15" />
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111 <param name="step_size" value="100" />
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112 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
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113 </test>
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114 </tests>
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115 <help>
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116 <![CDATA[
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117 **What it does**
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118
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119 Makes adjacent or sliding windows across a genome or BED file.
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120
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121 @REFERENCES@
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122 ]]>
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123 </help>
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124 <expand macro="citations" />
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125 </tool>