Mercurial > repos > devteam > column_maker

annotate column_maker.xml @ 6:0aeda7a81b46 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
author devteam
date Wed, 30 Dec 2020 00:49:52 +0000
parents c6fdc1118036
children e7c273e8d4d6
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6
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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1 <tool id="Add_a_column1" name="Compute" version="1.4">
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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2 <description>an expression on every row</description>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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3 <requirements>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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4 <requirement type="package" version="3.8">python</requirement>
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5 <requirement type="package" version="4.4">sed</requirement>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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6 <requirement type="package" version="1.19.1">numpy</requirement>
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7 </requirements>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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8 <command detect_errors="aggressive"><![CDATA[
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9 #if $header_lines_conditional.header_lines_select == "yes":
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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10 (sed -n '1,1p' '$input' | sed "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header &&
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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11 sed '1,1d' '$input' > data &&
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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12 #else:
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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13 touch header &&
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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14 ln -s '$input' data &&
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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15 #end if
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16
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17 ## inject colums and column_types metadata into inputs json
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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18 #import json
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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19 #set inputs_dict = json.load(open($inputs))
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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20 #set inputs_dict['columns'] = $input.metadata.columns
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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21 #set inputs_dict['column_types'] = $input.metadata.column_types
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22 #set x = json.dump($inputs_dict, open($inputs, 'w'))
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23
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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24 python '$__tool_directory__/column_maker.py'
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25 data column_maker_output
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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26 --load_json '$inputs'
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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27 && cat header column_maker_output > '$out_file1'
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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28 ]]></command>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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29 <configfiles>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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30 <inputs name="inputs"/>
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31 </configfiles>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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32 <inputs>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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33 <param name="cond" type="text" value="c3-c2" label="Add expression"/>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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34 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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35 <param name="round" type="select" label="Round result?">
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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36 <option value="no">NO</option>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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37 <option value="yes">YES</option>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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38 </param>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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39 <conditional name="header_lines_conditional">
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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40 <param name="header_lines_select" type="select" label="Skip a header line" help="# characters are already considered as comments and kept" >
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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41 <option value="no" >no</option>
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42 <option value="yes" >yes</option>
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43 </param>
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44 <when value="no">
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45 </when>
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46 <when value="yes">
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47 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
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48 </when>
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49 </conditional>
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50 <param name="avoid_scientific_notation" type="select" label="Avoid scientific notation" help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers).">
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51 <option value="no">no</option>
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52 <option value="yes">yes</option>
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53 </param>
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54 </inputs>
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55 <outputs>
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56 <data format_source="input" name="out_file1" metadata_source="input"/>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="cond" value="c3-c2"/>
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61 <param name="input" value="1.bed"/>
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62 <param name="round" value="no"/>
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63 <output name="out_file1" file="column_maker_out1.interval"/>
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64 </test>
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65 <test>
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66 <param name="cond" value="c4*1"/>
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67 <param name="input" value="1.interval"/>
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68 <param name="round" value="no"/>
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69 <output name="out_file1" file="column_maker_out2.interval"/>
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70 </test>
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71 <test>
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72 <param name="cond" value="c4*1"/>
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73 <param name="input" value="1.header.tsv"/>
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74 <param name="round" value="no"/>
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75 <conditional name="header_lines_conditional">
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76 <param name="header_lines_select" value="yes" />
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77 <param name="header_new_column_name" value="value1_again" />
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78 </conditional>
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79 <output name="out_file1" file="column_maker_out2.header.tsv"/>
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80 </test>
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81 <test>
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82 <param name="cond" value="c4*1"/>
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83 <param name="input" value="1.interval"/>
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84 <param name="round" value="yes"/>
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85 <output name="out_file1" file="column_maker_out3.interval"/>
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86 </test>
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87 <test>
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88 <param name="cond" value="float(.0000000000001)"/>
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89 <param name="input" value="1.bed"/>
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90 <param name="round" value="no"/>
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91 <output name="out_file1">
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92 <assert_contents>
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93 <has_text text="CCDS10397" />
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94 <has_text text="1e-13" />
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95 </assert_contents>
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96 </output>
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97 </test>
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98 <test>
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99 <param name="cond" value="float(.0000000000001)"/>
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100 <param name="input" value="1.bed"/>
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101 <param name="round" value="no"/>
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102 <param name="avoid_scientific_notation" value="yes"/>
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103 <output name="out_file1">
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104 <assert_contents>
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105 <has_text text="CCDS10397" />
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106 <has_text text=".0000000000001" />
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107 <not_has_text text="1e-13" />
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108 </assert_contents>
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109 </output>
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110 </test>
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111 </tests>
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112 <help>
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113
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114 .. class:: infomark
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115
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116 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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117
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118 -----
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119
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120 **What it does**
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121
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122 This tool computes an expression for every row of a dataset and appends the result as a new column (field).
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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123
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124 - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
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125
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126 - **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position
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127
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128 -----
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129
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130 **Example**
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131
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132 If this is your input::
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133
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134 chr1 151077881 151077918 2 200 -
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135 chr1 151081985 151082078 3 500 +
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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136
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137 computing "c4*c5" will produce::
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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138
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139 chr1 151077881 151077918 2 200 - 400.0
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140 chr1 151081985 151082078 3 500 + 1500.0
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141
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142 if, at the same time, "Round result?" is set to **YES** results will look like this::
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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143
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144 chr1 151077881 151077918 2 200 - 400
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145 chr1 151081985 151082078 3 500 + 1500
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146
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147 You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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148
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149 chr1 151077881 151077918 2 200 - True
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150 chr1 151081985 151082078 3 500 + True
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151
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152 or computing "type(c2)==type('') for Input will return::
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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153
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154 chr1 151077881 151077918 2 200 - False
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155 chr1 151081985 151082078 3 500 + False
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156
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157
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158 The following built-in functions are available::
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159
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160 abs | all | any | bin | bool | chr | ceil | cmp | complex
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161
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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162 divmod | exp | float | log | log10 | floor | hex | int | len | long
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163
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164 max | min | oct | ord | pow | range | reversed
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165
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166 round | sorted | sqrt | str | sum | type | unichr | unicode |
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167
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168 </help>
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169 <citations />
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170 </tool>