Mercurial > repos > bgruening > split_file_on_column

annotate split_file_on_column.xml @ 0:f30aca50efbb draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty
author bgruening
date Wed, 26 Aug 2015 07:31:55 -0400
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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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1 <tool id="tp_split_on_column" name="Split file" version="0.2">
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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="4.1.0">gnu_awk</requirement>
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5 </requirements>
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6 <command>
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7 <![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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8 awk -F'\t' '{print > \$$column ".$infile.ext" }' $infile
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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9 ]]>
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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10 </command>
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11 <inputs>
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12 <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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13 <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
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 </inputs>
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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15 <outputs>
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16 <collection name="split_output" type="list" label="Table split on first 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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17 <discover_datasets pattern="__name_and_ext__" directory="." />
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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18 </collection>
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19 </outputs>
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20 <!--outputs>
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21 <data format="input" name="outfile" metadata_source="infile" label="${tool.name} on ${on_string}"/>
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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22 </outputs-->
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23 <tests>
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24 <test>
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25 <param name="infile" value="5cols.tabular" ftype="tabular"/>
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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26 <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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27 <output_collection name="split_output" type="list">
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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28 <element name="1">
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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29 <assert_contents>
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30 <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" />
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 </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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32 </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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33 <element name="2">
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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34 <assert_contents>
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35 <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" />
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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36 </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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37 </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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38 </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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39 </test>
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40 </tests>
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41 <help>
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42 <![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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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 **What it does**
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45
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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46 This tool splits a file into different smaller files using a specific column.
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47 It will work like the group tool, but every group is saved to its own file.
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 -----
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50
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 **Example**
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52
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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53 Splitting on column 5 from this::
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54
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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55 chr7 56632 56652 cluster 1
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56 chr7 56736 56756 cluster 1
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57 chr7 56761 56781 cluster 2
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58 chr7 56772 56792 cluster 2
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59 chr7 56775 56795 cluster 2
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60
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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61 will produce 2 files with different clusters::
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62
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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63 chr7 56632 56652 cluster 1
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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64 chr7 56736 56756 cluster 1
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65
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66
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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67 chr7 56761 56781 cluster 2
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68 chr7 56772 56792 cluster 2
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69 chr7 56775 56795 cluster 2
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71
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72 ]]>
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73 </help>
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74 </tool>