Mercurial > repos > bgruening > replace_column_by_key_value_file

annotate replaceColumn.xml @ 1:d533e4b75800 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
author bgruening
date Sun, 23 Sep 2018 04:03:34 -0400
parents cc18bac5afdb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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1 <tool id="replace_column_with_key_value_file" name="Replace column" version="0.2">
0
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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2 <description>by values which are defined in a convert file</description>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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3 <command>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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4 <![CDATA[
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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5 python '$replaceColumnScript'
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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6 ]]>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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7 </command>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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8 <configfiles>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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9 <configfile name="replaceColumnScript">
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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10 <![CDATA[
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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11 import sys
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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12
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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13 replace_file = '$replace_information'
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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14 original_file = '$original_file'
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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15 column = int("$column_replace") - 1
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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16 ignore_start_lines = int("$skip_lines")
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d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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17 delimiter_local = "\t" if str("$delimiter") == "tab" else str("$delimiter")
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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18 comment_str = str("$pass_comments")
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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19 unk_strat = str("$unknowns_strategy")
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20
1
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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21 ## read conversion information to index
0
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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22 conversion = {}
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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23
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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24 with open(replace_file, 'r') as conversion_file:
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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25 for line in conversion_file:
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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26 conv_key_value = line.strip().split()
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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27 if len(conv_key_value) == 2:
1
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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28 conversion[conv_key_value[0]] = conv_key_value[1]
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cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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29
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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30 ## read file line by line, search for column entry if it can be replaced. Otherwise it will be skipped.
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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31 with open("output_file", 'w') as output:
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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32 with open(original_file) as original:
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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33 for i, line in enumerate(original):
1
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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34 if i < ignore_start_lines or (comment_str and line.startswith(comment_str)):
0
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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35 output.write(line)
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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36 continue
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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37
1
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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38 line_content = line.rstrip().split(delimiter_local)
0
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39
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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40 out = list()
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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41 for j, line_content_column in enumerate(line_content):
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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42 if j == column:
1
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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43
0
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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44 if line_content_column in conversion:
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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45 out.append(conversion[line_content_column])
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d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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46 elif unk_strat == "print":
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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47 out.append(line_content_column)
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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48 elif unk_strat == "error":
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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49 raise Exception('ERROR: Encountered a value [%s] in the file that is not in the replacements file and is not commented with [%s]' % (line_content_column, comment_str))
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cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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50 else:
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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51 out.append(line_content_column)
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52
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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53 if len(out) == len(line_content):
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54 output.write('%s\n' % delimiter_local.join(out))
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55
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56 ]]>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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57 </configfile>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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58 </configfiles>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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59 <inputs>
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60 <param name="original_file" type="data" format="tabular"
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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61 label="File in which you want to replace some values"
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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62 help="The entries of a specific column are replaced by the information given by the next input file." />
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63 <param name="replace_information" type="data" format="tabular"
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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64 label="Replace information file"
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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65 help="This file contains in the first column the entries that should be replaced by the values of the second column." />
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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66 <param name="column_replace" type="data_column" data_ref="original_file" multiple="false"
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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67 label="Which column should be replaced?" />
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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68 <param name="skip_lines" type='integer' value='0' label="Skip this many starting lines" />
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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69 <param name="delimiter" type="select" label="Delimited by">
1
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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70 <option value="tab" selected="True">Tab</option>
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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71 <option value=" ">Space</option>
0
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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72 <option value=".">Dot</option>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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73 <option value=",">Comma</option>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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74 <option value="-">Dash</option>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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75 <option value="_">Underscore</option>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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76 <option value="|">Pipe</option>
cc18bac5afdb planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4
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77 </param>
1
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78 <param name="unknowns_strategy" type="select" label="When an unknown value is encountered">
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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79 <option value="skip" selected="True">Skip / Do not print</option>
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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80 <option value="print">Print without modification</option>
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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81 <option value="error">Exit with an error</option>
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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82 </param>
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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83 <param name="pass_comments" type="text" value="#" label="Do not perform replacement on lines starting with">
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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84 <sanitizer>
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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85 <valid>
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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86 <add value="#" />
d533e4b75800 planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 0def21576e206a0732ce63bacd18533064ddf155
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87 </valid>
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88 </sanitizer>
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89 </param>
0
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90 </inputs>
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91 <outputs>
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92 <data name="outfile_replace" format="txt" from_work_dir="output_file"/>
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93 </outputs>
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94 <tests>
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95 <test>
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96 <param name="replace_information" value="GRCh38_ensembl2UCSC.txt" ftype="tabular" />
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97 <param name="original_file" value="original_file" ftype="tabular" />
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98 <param name="column_replace" value="1"/>
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99 <param name="skip_lines" value="1"/>
1
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100 <param name="delimiter" value="tab" />
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101 <param name="unknowns_strategy" value="skip"/>
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102 <param name="pass_comments" value="#"/>
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103 <output name="outfile_replace" file="result_file"/>
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104 </test>
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105 <test>
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106 <param name="replace_information" value="GRCh38_ensembl2UCSC.txt" ftype="tabular" />
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107 <param name="original_file" value="empty_mapping" ftype="tabular" />
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108 <param name="column_replace" value="1"/>
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109 <param name="skip_lines" value="1"/>
1
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110 <param name="delimiter" value="tab" />
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111 <param name="unknowns_strategy" value="skip"/>
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112 <param name="pass_comments" value="#"/>
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113 <output name="outfile_replace" file="result_file_empty_mapping"/>
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114 </test>
1
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115 <test expect_failure="True">
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116 <param name="replace_information" value="neg_test_map.txt" ftype="tabular" />
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117 <param name="original_file" value="neg_test_commented.txt" ftype="tabular" />
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118 <param name="column_replace" value="1"/>
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119 <param name="skip_lines" value="0"/>
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120 <param name="delimiter" value="tab" />
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121 <param name="unknowns_strategy" value="error"/>
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122 <param name="pass_comments" value="#"/>
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123 </test>
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124 <test>
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125 <param name="replace_information" value="neg_test_map.txt" ftype="tabular" />
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126 <param name="original_file" value="neg_test_commented.txt" ftype="tabular" />
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127 <param name="column_replace" value="1"/>
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128 <param name="skip_lines" value="0"/>
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129 <param name="delimiter" value="tab" />
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130 <param name="unknowns_strategy" value="print"/>
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131 <param name="pass_comments" value="#"/>
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132 <output name="outfile_replace" file="neg_test_commented.txt"/>
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133 </test>
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134 </tests>
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135 <help>
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136 <![CDATA[
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137 **What it does**
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138
1
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139 This tool replaces the entries of a defined column with entries given by a replacement file.
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140 For example the replacement file holds the information of the naming scheme of ensembl annotated chromosomes in the frist column and in the second the UCSC annotation.
0
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141 A file which is having information about chromosomes in ensembl notation in column x can now be converted to a file which holds the same information but in UCSC annotation.
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142
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143 A useful repository for ensembl and UCSC chromosomes mapping is: https://github.com/dpryan79/ChromosomeMappings
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144 ]]>
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145 </help>
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146 </tool>