Mercurial > repos > bgruening > split_file_on_column

annotate split_file_on_column.xml @ 2:bddc7c1070d2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 62597aa4ecda3de4ebdf8794d83a494e32148b11
author bgruening
date Sat, 10 Dec 2016 15:51:55 -0500
parents b1914e537f3e
children 61e58789650e
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bddc7c1070d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 62597aa4ecda3de4ebdf8794d83a494e32148b11
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1 <tool id="tp_split_on_column" name="Split file" version="0.3">
0
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2 <description>according to the values of a column</description>
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3 <requirements>
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4 <requirement type="package" version="4.1.3">gawk</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
1
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8 mkdir tmp_out &&
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bddc7c1070d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 62597aa4ecda3de4ebdf8794d83a494e32148b11
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9 awk -F'\t' '{print > "tmp_out/"\$$column".$infile.ext" }' '$infile'
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10 ]]>
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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11 </command>
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12 <inputs>
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13 <param format="tabular" name="infile" type="data" label="File to select" />
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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14 <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
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15 </inputs>
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16 <outputs>
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17 <collection name="split_output" type="list" label="Table split on first column">
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18 <discover_datasets pattern="__name_and_ext__" directory="tmp_out" />
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19 </collection>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="infile" value="5cols.tabular" ftype="tabular"/>
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24 <param name="column" value="5" />
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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25 <output_collection name="split_output" type="list">
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26 <element name="1">
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27 <assert_contents>
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28 <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" />
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29 </assert_contents>
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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30 </element>
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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31 <element name="2">
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32 <assert_contents>
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33 <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" />
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34 </assert_contents>
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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35 </element>
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36 </output_collection>
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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37 </test>
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38 </tests>
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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39 <help>
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40 <![CDATA[
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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42 **What it does**
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43
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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44 This tool splits a file into different smaller files using a specific column.
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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45 It will work like the group tool, but every group is saved to its own file.
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46
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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47 -----
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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48
f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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49 **Example**
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f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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51 Splitting on column 5 from this::
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53 chr7 56632 56652 cluster 1
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54 chr7 56736 56756 cluster 1
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55 chr7 56761 56781 cluster 2
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56 chr7 56772 56792 cluster 2
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57 chr7 56775 56795 cluster 2
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58
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59 will produce 2 files with different clusters::
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61 chr7 56632 56652 cluster 1
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62 chr7 56736 56756 cluster 1
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f30aca50efbb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
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65 chr7 56761 56781 cluster 2
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66 chr7 56772 56792 cluster 2
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67 chr7 56775 56795 cluster 2
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70 ]]>
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71 </help>
2
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72 <citations>
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73 </citations>
0
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74 </tool>