Mercurial > repos > devteam > column_maker

annotate column_maker.xml @ 8:227e82286a0e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
author devteam
date Wed, 24 Feb 2021 05:19:12 +0000
parents e7c273e8d4d6
children 33b81f9ea109
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8
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1 <tool id="Add_a_column1" name="Compute" version="1.6">
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2 <description>an expression on every row</description>
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3 <requirements>
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4 <requirement type="package" version="3.8">python</requirement>
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5 <requirement type="package" version="1.19.1">numpy</requirement>
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6 </requirements>
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7 <command detect_errors="aggressive"><![CDATA[
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8 ln -s '$input' data &&
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9
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10 ## inject colums and column_types metadata into inputs json
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11 #import json
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12 #set inputs_dict = json.load(open($inputs))
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13 #set inputs_dict['columns'] = $input.metadata.columns
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14 #set inputs_dict['column_types'] = $input.metadata.column_types
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15 ## flatten conditional
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16 #if $header_lines_conditional.header_lines_select == "yes":
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17 #set inputs_dict['header_new_column_name'] = str($header_lines_conditional.header_new_column_name)
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18 #end if
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19 #set x = json.dump($inputs_dict, open($inputs, 'w'))
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20
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21 python '$__tool_directory__/column_maker.py'
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22 data '$out_file1'
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23 --load_json '$inputs'
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24 ]]></command>
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25 <configfiles>
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26 <inputs name="inputs"/>
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27 </configfiles>
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28 <inputs>
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29 <param name="cond" type="text" value="c3-c2" label="Add expression">
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30 <sanitizer>
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31 <valid initial="default">
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32 <add value="&lt;" />
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33 <add value="&gt;" />
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34 <add value="&quot;" />
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35 <add value="&apos;" />
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36 </valid>
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37 </sanitizer>
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38 </param>
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39 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
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40 <param name="round" type="boolean" truevalue="yes" falsevalue="no" label="Round result?" />
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41 <param name="avoid_scientific_notation" type="boolean" truevalue="yes" falsevalue="no"
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42 label="Avoid scientific notation"
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43 help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers)." />
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44 <conditional name="header_lines_conditional">
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45 <param name="header_lines_select" type="select"
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46 label="Input has a header line with column names?"
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47 help="Select Yes to be able to specify a name for the new column and have it added to the header line. If you select No, the first line will be treated as a regular line: If it is empty or starts with a # character it will be skipped, otherwise the tool will attempt to compute the specified expression on it." >
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48 <option value="no" >No</option>
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49 <option value="yes" >Yes</option>
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50 </param>
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51 <when value="no">
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52 </when>
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53 <when value="yes">
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54 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
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55 </when>
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56 </conditional>
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57 </inputs>
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58 <outputs>
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59 <data format_source="input" name="out_file1" metadata_source="input"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="cond" value="c3-c2"/>
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64 <param name="input" value="1.bed"/>
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65 <param name="round" value="false"/>
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66 <output name="out_file1" file="column_maker_out1.interval"/>
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67 </test>
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68 <test>
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69 <param name="cond" value="c4*1"/>
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70 <param name="input" value="1.interval"/>
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71 <param name="round" value="false"/>
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72 <output name="out_file1" file="column_maker_out2.interval"/>
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73 </test>
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74 <test>
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75 <param name="cond" value="c4*1"/>
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76 <param name="input" value="1.header.tsv"/>
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77 <param name="round" value="false"/>
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78 <conditional name="header_lines_conditional">
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79 <param name="header_lines_select" value="yes" />
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80 <param name="header_new_column_name" value="value1_again" />
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81 </conditional>
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82 <output name="out_file1" file="column_maker_out2.header.tsv"/>
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83 </test>
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84 <test>
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85 <param name="cond" value="c4*1"/>
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86 <param name="input" value="1.interval"/>
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87 <param name="round" value="true"/>
6
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88 <output name="out_file1" file="column_maker_out3.interval"/>
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89 </test>
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90 <test>
8
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91 <!-- test that single column input works -->
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92 <param name="cond" value="c1/10"/>
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93 <param name="input" value="1.tab" ftype="tabular"/>
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94 <param name="round" value="no"/>
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95 <output name="out_file1" file="column_maker_out4.tab"/>
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96 </test>
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97 <test>
6
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98 <param name="cond" value="float(.0000000000001)"/>
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99 <param name="input" value="1.bed"/>
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100 <param name="round" value="false"/>
6
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101 <output name="out_file1">
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102 <assert_contents>
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103 <has_text text="CCDS10397" />
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104 <has_text text="1e-13" />
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105 </assert_contents>
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106 </output>
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107 </test>
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108 <test>
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109 <param name="cond" value="float(.0000000000001)"/>
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110 <param name="input" value="1.bed"/>
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111 <param name="round" value="false"/>
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112 <param name="avoid_scientific_notation" value="true"/>
6
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113 <output name="out_file1">
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114 <assert_contents>
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115 <has_text text="CCDS10397" />
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116 <has_text text=".0000000000001" />
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117 <not_has_text text="1e-13" />
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118 </assert_contents>
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119 </output>
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120 </test>
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121 </tests>
8
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122 <help><![CDATA[
6
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123
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124 .. class:: infomark
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125
8
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126 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
6
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127
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128 -----
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129
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130 **What it does**
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131
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132 This tool computes an expression for every row of a dataset and appends the result as a new column (field).
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133
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134 - 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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135
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136 - **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position
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137
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138 -----
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139
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140 **Example**
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141
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142 If this is your input::
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143
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144 chr1 151077881 151077918 2 200 -
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145 chr1 151081985 151082078 3 500 +
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146
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147 computing "c4*c5" will produce::
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148
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149 chr1 151077881 151077918 2 200 - 400.0
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150 chr1 151081985 151082078 3 500 + 1500.0
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151
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152 if, at the same time, "Round result?" is set to **YES** results will look like this::
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153
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154 chr1 151077881 151077918 2 200 - 400
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155 chr1 151081985 151082078 3 500 + 1500
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156
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157 You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
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158
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159 chr1 151077881 151077918 2 200 - True
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160 chr1 151081985 151082078 3 500 + True
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161
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162 or computing "type(c2)==type('') for Input will return::
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163
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164 chr1 151077881 151077918 2 200 - False
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165 chr1 151081985 151082078 3 500 + False
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166
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167
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168 The following built-in functions are available::
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169
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170 abs | all | any | bin | bool | chr | ceil | cmp | complex
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171
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172 divmod | exp | float | log | log10 | floor | hex | int | len | long
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173
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174 max | min | oct | ord | pow | range | reversed
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175
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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176 round | sorted | sqrt | str | sum | type | unichr | unicode |
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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177
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178 ]]></help>
6
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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179 <citations />
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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180 </tool>