Mercurial > repos > bgruening > split_file_on_column

annotate split_file_on_column.xml @ 6:ff2a81aa3f08 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 6a2deb2f38472a2845123bd54e73b6bd115b3a0b
author bgruening
date Tue, 19 Jul 2022 13:25:20 +0000
parents d4b5b70e82cb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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ff2a81aa3f08 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 6a2deb2f38472a2845123bd54e73b6bd115b3a0b
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1 <tool id="tp_split_on_column" name="Split by group" version="0.6">
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2 <requirements>
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3 <requirement type="package" version="5.1.0">gawk</requirement>
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4 </requirements>
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5 <command>
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6 <![CDATA[
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7 mkdir tmp_out &&
37a53100b67e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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8 #if $include_header
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ff2a81aa3f08 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 6a2deb2f38472a2845123bd54e73b6bd115b3a0b
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9 awk -F '\t' 'NR==1{hdr=$0;next}f!="tmp_out/"\$$column".$infile.ext"{if(f) close(f); f="tmp_out/"\$$column".$infile.ext"}; {if (!seen[f]++) print hdr>f; print >> f}' $infile
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37a53100b67e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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10 #else
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11 awk -F'\t' '{print >> "tmp_out/"\$$column".$infile.ext" }' '$infile'
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12 #end if
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param format="tabular" name="infile" type="data" label="File to split" />
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17 <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
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18
5
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19 <param name="include_header" type="boolean" label="Include header in splits?"
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20 help="Include the first line (the assumed header line) to all split files." />
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21 </inputs>
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22 <outputs>
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23 <collection name="split_output" type="list" label="Split by group collection">
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24 <discover_datasets pattern="__name_and_ext__" directory="tmp_out" />
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25 </collection>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="infile" value="5cols.tabular" ftype="tabular"/>
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30 <param name="column" value="5" />
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31 <param name="include_header" value="false"/>
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32 <output_collection name="split_output" type="list">
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33 <element name="1">
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34 <assert_contents>
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35 <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" />
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36 </assert_contents>
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37 </element>
37a53100b67e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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38 <element name="2">
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39 <assert_contents>
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40 <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" />
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41 </assert_contents>
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42 </element>
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43 </output_collection>
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44 </test>
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45 <test>
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46 <param name="infile" value="5cols-with-header.tabular" ftype="tabular" />
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47 <param name="column" value="5" />
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48 <param name="include_header" value="true"/>
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49 <output_collection name="split_output" type="list">
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50 <element name="1">
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51 <assert_contents>
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52 <has_line_matching expression="Column1\tColumn2\tColumn3\tColumn4\tColumn5" />
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53 <has_n_lines n="3" />
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54 <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" />
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55 </assert_contents>
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56 </element>
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57 <element name="2">
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58 <assert_contents>
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59 <has_line_matching expression="Column1\tColumn2\tColumn3\tColumn4\tColumn5" />
37a53100b67e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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60 <has_n_lines n="4" />
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61 <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" />
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62 </assert_contents>
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63 </element>
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64 </output_collection>
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65 </test>
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66 <test>
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67 <param name="infile" value="5cols-with-header.tabular" ftype="tabular" />
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68 <param name="column" value="5" />
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69 <param name="include_header" value="false"/>
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70 <output_collection name="split_output" type="list">
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71 <element name="1">
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72 <assert_contents>
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73 <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" />
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74 </assert_contents>
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75 </element>
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76 <element name="2">
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77 <assert_contents>
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78 <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" />
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79 </assert_contents>
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80 </element>
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81 </output_collection>
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82 </test>
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83 <test><!-- test with unsorted column, no header -->
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84 <param name="infile" value="5cols-unsorted.tabular" ftype="tabular" />
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85 <param name="column" value="5" />
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86 <param name="include_header" value="false"/>
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87 <output_collection name="split_output" type="list">
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88 <element name="1">
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89 <assert_contents>
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90 <has_n_lines n="3" />
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91 </assert_contents>
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92 </element>
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93 <element name="2">
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94 <assert_contents>
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95 <has_n_lines n="2" />
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96 </assert_contents>
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97 </element>
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98 </output_collection>
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99 </test>
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100 <test><!-- test with unsorted column, with header -->
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101 <param name="infile" value="5cols-unsorted-with-header.tabular" ftype="tabular" />
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102 <param name="column" value="5" />
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103 <param name="include_header" value="true"/>
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104 <output_collection name="split_output" type="list">
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105 <element name="1">
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106 <assert_contents>
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107 <has_n_lines n="4" />
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108 <has_line_matching expression="Column1\tColumn2\tColumn3\tColumn4\tColumn5" />
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109
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110 </assert_contents>
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111 </element>
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112 <element name="2">
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113 <assert_contents>
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114 <has_n_lines n="3" />
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115 <has_line_matching expression="Column1\tColumn2\tColumn3\tColumn4\tColumn5" />
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116 </assert_contents>
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117 </element>
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118 </output_collection>
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119 </test>
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120 </tests>
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121 <help>
2
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122 <![CDATA[
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123
5
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124 ========
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125 Synopsis
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126 ========
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127
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128 Given a single input dataset this tool splits the file on unique values from a specified column.
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129
5
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130 ===========
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131 Description
d4b5b70e82cb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit df81dd26ed1cf67a0d95b9614738b1d59667773f
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132 ===========
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133
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134 This tool splits a file into a collection based on unique values of a speific column.
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135 It performs a grouping operation with every group saved as a separate collection element.
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136 You have the option to include the header (first line) to all splits.
4
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137 If you have a header and don't want keep it, please remove it before you use this tool.
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138 For example with the "Remove beginning of a file" tool.
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139
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140 -----
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141
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142 **Example**
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143
5
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144 Splitting this file on column 1::
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145
5
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146 chr1 10 20
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147 chr1 30 40
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148 chr2 40 70
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149 chr4 60 80
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150
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151
6
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152 will produce a collection with 3 elements::
5
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153
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154 chr1 10 20
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155 chr1 30 40
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156
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157 chr2 40 70
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158
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159 chr4 60 80
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160
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161 ------
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162
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163 .. image:: $PATH_TO_IMAGES/split_by_group.svg
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164 :width: 800
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165 :alt: Split by group
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166
2
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167 ]]>
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168 </help>
4
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169 <citations>
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170 <citation type="bibtex">
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171 @misc{githubsplit_file_on_column,
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172 author = {Gruening, Bjoern},
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173 year = {2015},
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174 title = {split_file_on_column},
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175 publisher = {GitHub},
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176 journal = {GitHub repository},
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177 url = {https://github.com/bgruening/galaxytools},
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178 }
37a53100b67e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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179 </citation>
37a53100b67e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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180 </citations>
0
ad6a989924ac Uploaded
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181 </tool>
4
37a53100b67e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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