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annotate makeWindowsBed.xml @ 43:07e8b80f278c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author iuc
date Fri, 01 Apr 2022 19:02:51 +0000
parents 7ab85ac5f64b
children
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3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>make interval windows across a genome</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="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 bedtools makewindows
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11 #if $type.type_select == 'genome':
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12 @GENOME_FILE_MAKEWINDOWS@
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13 #else:
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14 -b '$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 #end if
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24 $sourcename
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25 > '$output'
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26 ]]></command>
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27 <inputs>
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28 <conditional name="type">
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29 <param name="type_select" type="select" label="Work with">
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30 <option value="bed" selected="true">Bed File</option>
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31 <option value="genome">Genome File</option>
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32 </param>
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33 <when value="bed">
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34 <param name="input" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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35 </when>
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36 <when value="genome">
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37 <expand macro="input_conditional_genome_file" />
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38 </when>
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39 </conditional>
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40 <conditional name="action">
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41 <param name="action_select" type="select" label="Work with">
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42 <option value="windowsize" selected="true">Set WindowSize</option>
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43 <option value="number">Give Number of Windows</option>
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44 </param>
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45 <when value="windowsize">
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46 <param name="windowsize" argument="-w" type="integer" value="1"
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47 label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
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48 help="i.e. same number of nucleotide in each window" />
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49 <conditional name="step_size">
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50 <param name="step_size_select" type="select"
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51 label="Specify Step size? i.e. how many base pairs to step before creating a new window"
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52 help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
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53 <option value="yes">Yes</option>
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54 <option value="no" selected="true">No</option>
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55 </param>
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56 <when value="yes">
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57 <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
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58 </when>
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59 <when value="no" />
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60 </conditional>
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61 </when>
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62 <when value="number">
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63 <param name="number" argument="-n" type="integer" value="1"
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64 label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows"
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65 help="I.e. same number of windows, with varying window sizes" />
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66 </when>
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67 </conditional>
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68 <param name="sourcename" type="select" label="ID Naming Options">
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69 <option value="" selected="true">Default</option>
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70 <option value="-i src">use the source interval's name</option>
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71 <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
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72 <option value="-i srcwinnum">use the source interval's name with the window number.</option>
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73 </param>
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74 </inputs>
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75 <outputs>
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76 <data name="output" format="bed" />
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77 </outputs>
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78 <tests>
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79 <test>
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80 <param name="type_select" value="genome" />
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81 <param name="genome_file_opts_selector" value="hist" />
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82 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
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83 <param name="action_select" value="windowsize" />
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84 <param name="windowsize" value="1000000" />
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85 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
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86 </test>
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87 <test>
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88 <param name="type_select" value="genome" />
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89 <param name="genome_file_opts_selector" value="hist" />
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90 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
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91 <param name="action_select" value="windowsize" />
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92 <param name="windowsize" value="1000000" />
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93 <param name="step_size_select" value="yes" />
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94 <param name="step_size" value="50000" />
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95 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
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96 </test>
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97 <test>
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98 <param name="type_select" value="genome" />
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99 <param name="genome_file_opts_selector" value="hist" />
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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 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
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104 </test>
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105 <test>
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106 <param name="type_select" value="bed" />
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107 <param name="input" value="makeWindowBed1.bed" ftype="bed" />
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108 <param name="action_select" value="number" />
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109 <param name="number" value="15" />
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110 <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
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111 </test>
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112 </tests>
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113 <help><![CDATA[
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114 **What it does**
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115
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116 Makes adjacent or sliding windows across a genome or BED file.
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117
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118 @REFERENCES@
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119 ]]></help>
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120 <expand macro="citations" />
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121 </tool>