Mercurial > repos > bgruening > split_file_on_column

annotate split_file_on_column.xml @ 4:37a53100b67e draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
author bgruening
date Thu, 25 Feb 2021 15:54:13 +0000
parents b60f2452580e
children d4b5b70e82cb
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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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1 <tool id="tp_split_on_column" name="Split file" version="0.4">
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2 <description>according to the values of a column</description>
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3 <requirements>
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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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4 <requirement type="package" version="5.0.1">gawk</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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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8 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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9 #if $include_header
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 awk -F '\t' 'NR==1{hdr=$0;next}f!="tmp_out/"\$$column".$infile.ext"{if(f) close(f); f="tmp_out/"\$$column".$infile.ext";print hdr>f} {print >> f}' $infile
37a53100b67e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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11 #else
37a53100b67e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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12 awk -F'\t' '{print > "tmp_out/"\$$column".$infile.ext" }' '$infile'
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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13 #end if
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param format="tabular" name="infile" type="data" label="File to select" />
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18 <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
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19
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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20 <param name="include_header" type="boolean" label="Include the header in all splitted files?"
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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21 help="Include the first line (the assumed header line) in all splitted files." />
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22 </inputs>
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23 <outputs>
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24 <collection name="split_output" type="list" label="Table split on first column">
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25 <discover_datasets pattern="__name_and_ext__" directory="tmp_out" />
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26 </collection>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="infile" value="5cols.tabular" ftype="tabular"/>
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31 <param name="column" value="5" />
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32 <param name="include_header" value="false"/>
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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33 <output_collection name="split_output" type="list">
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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34 <element name="1">
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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35 <assert_contents>
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36 <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" />
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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37 </assert_contents>
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38 </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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39 <element name="2">
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40 <assert_contents>
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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41 <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" />
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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42 </assert_contents>
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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43 </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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44 </output_collection>
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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45 </test>
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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46 <test>
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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47 <param name="infile" value="5cols-with-header.tabular" ftype="tabular" />
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48 <param name="column" value="5" />
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49 <param name="include_header" value="true"/>
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50 <output_collection name="split_output" type="list">
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51 <element name="1">
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52 <assert_contents>
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53 <has_line_matching expression="Column1\tColumn2\tColumn3\tColumn4\tColumn5" />
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54 <has_n_lines n="3" />
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55 <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" />
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56 </assert_contents>
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57 </element>
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58 <element name="2">
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59 <assert_contents>
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60 <has_line_matching expression="Column1\tColumn2\tColumn3\tColumn4\tColumn5" />
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61 <has_n_lines n="4" />
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62 <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" />
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63 </assert_contents>
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64 </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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65 </output_collection>
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66 </test>
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67 <test>
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68 <param name="infile" value="5cols-with-header.tabular" ftype="tabular" />
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69 <param name="column" value="5" />
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70 <param name="include_header" value="false"/>
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71 <output_collection name="split_output" type="list">
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72 <element name="1">
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73 <assert_contents>
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74 <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" />
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75 </assert_contents>
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76 </element>
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77 <element name="2">
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78 <assert_contents>
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79 <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" />
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80 </assert_contents>
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81 </element>
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82 </output_collection>
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83 </test>
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84 </tests>
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85 <help>
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86 <![CDATA[
0
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87
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88 **What it does**
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89
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90 This tool splits a file into different smaller files using a specific column.
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91 It will work like the group tool, but every group is saved to its own file.
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92 You have the option to include the header (first line) in all splitted files.
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93 If you have a header and don't want keep it, please remove it before you use this tool.
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94 For example with the "Remove beginning of a file" tool.
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95
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96 -----
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97
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98 **Example**
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99
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100 Splitting a file without header on column 5 from this::
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101
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102 chr7 56632 56652 cluster 1
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103 chr7 56736 56756 cluster 1
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104 chr7 56761 56781 cluster 2
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105 chr7 56772 56792 cluster 2
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106 chr7 56775 56795 cluster 2
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107
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108 will produce 2 files with different clusters::
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109
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110 chr7 56632 56652 cluster 1
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111 chr7 56736 56756 cluster 1
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112
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113
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114 chr7 56761 56781 cluster 2
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115 chr7 56772 56792 cluster 2
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116 chr7 56775 56795 cluster 2
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117
2
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118 ]]>
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119 </help>
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120 <citations>
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121 <citation type="bibtex">
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122 @misc{githubsplit_file_on_column,
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123 author = {Gruening, Bjoern},
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124 year = {2015},
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125 title = {split_file_on_column},
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126 publisher = {GitHub},
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127 journal = {GitHub repository},
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128 url = {https://github.com/bgruening/galaxytools},
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129 }
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130 </citation>
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131 </citations>
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132 </tool>
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133