Mercurial > repos > devteam > column_maker
annotate column_maker.xml @ 9:6595517c2dd8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
author | iuc |
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date | Thu, 28 Jul 2022 15:28:30 +0000 |
parents | 02026300aa45 |
children | aff5135563c6 |
rev | line source |
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9
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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1 <tool id="Add_a_column1" name="Compute" version="2.0"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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2 <description>on rows</description> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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3 <macros> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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4 <xml name="compute_repeat"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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5 <repeat name="expressions" title="Expressions" min="1" default="1"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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6 <param name="cond" type="text" value="c3-c2" label="Add expression"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
|
7 <sanitizer> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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8 <valid initial="default"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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9 <add value="<" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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10 <add value=">" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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11 <add value=""" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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12 <add value="'" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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13 </valid> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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14 </sanitizer> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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15 </param> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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16 <conditional name="add_column"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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17 <param name="mode" type="select" label="Mode of the operation"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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18 <option value="">Append</option> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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diff
changeset
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19 <option value="I">Insert</option> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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20 <option value="R">Replace</option> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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21 </param> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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22 <when value=""> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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23 <param name="pos" type="hidden" value="" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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24 </when> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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25 <when value="I"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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26 <param name="pos" type="integer" min="1" value="1" label="Insert new column before existing column number" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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27 </when> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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28 <when value="R"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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29 <param name="pos" type="integer" min="1" value="1" label="Use new column to replace column number" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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30 </when> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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31 </conditional> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
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32 <yield /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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33 </repeat> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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34 </xml> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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changeset
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35 </macros> |
5
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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changeset
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36 <requirements> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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37 <requirement type="package" version="3.8">python</requirement> |
9
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
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38 <requirement type="package" version="1.23.1">numpy</requirement> |
5
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
4
diff
changeset
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39 </requirements> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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40 <command detect_errors="aggressive"><![CDATA[ |
9
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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diff
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41 python '$__tool_directory__/column_maker.py' |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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diff
changeset
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42 #if str($error_handling.auto_col_types) == 'on': |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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diff
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43 #set $col_types = $input.metadata.column_types |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
changeset
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44 #else: |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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diff
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45 #set $col_types = ','.join(['str' for t in $input.metadata.column_types.split(',')]) |
8
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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46 #end if |
9
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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47 --column-types $col_types |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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48 $avoid_scientific_notation |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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diff
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49 #if str($ops.header_lines_select) == 'yes': |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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50 --header |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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51 #end if |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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52 --file '$expressions_file' |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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53 $error_handling.fail_on_non_existent_columns |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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diff
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54 $error_handling.non_computable.action |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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diff
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55 #if str($error_handling.non_computable.action) == '--non-computable-default': |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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56 '$error_handling.non_computable.default_value' |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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57 #end if |
8
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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58 '$input' |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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59 '$out_file1' |
5
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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60 ]]></command> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
4
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61 <configfiles> |
9
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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62 <configfile name="expressions_file"><![CDATA[ |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
8
diff
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63 #if str($ops.header_lines_select) == 'yes': |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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64 #for $expr in $ops.expressions: |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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65 ${expr.cond};${expr.add_column.pos}${expr.add_column.mode};${expr.new_column_name} |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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66 #end for |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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67 #else: |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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68 #for $expr in $ops.expressions: |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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69 ${expr.cond};${expr.add_column.pos}${expr.add_column.mode}; |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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70 #end for |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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71 #end if |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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72 ]]></configfile> |
5
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
4
diff
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73 </configfiles> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
4
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74 <inputs> |
9
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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75 <param name="input" type="data" format="tabular" label="Input file" help="Dataset missing? See TIP below" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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76 <conditional name="ops"> |
6
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
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77 <param name="header_lines_select" type="select" |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents:
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78 label="Input has a header line with column names?" |
9
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents:
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79 help="Select Yes to be able to specify names for new columns and have them added to the header line. If you select No, the first line will be treated as a regular line: If it is empty or starts with a # character it will be skipped, otherwise the tool will attempt to compute the specified expression on it." > |
8
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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80 <option value="no">No</option> |
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81 <option value="yes">Yes</option> |
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82 </param> |
9
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83 <when value="no"> |
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84 <expand macro="compute_repeat" /> |
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85 </when> |
5
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86 <when value="yes"> |
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87 <expand macro="compute_repeat"> |
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88 <param name="new_column_name" type="text" value="New Column" label="The new column name" /> |
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89 </expand> |
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90 </when> |
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91 </conditional> |
9
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92 <param name="avoid_scientific_notation" type="boolean" truevalue="--avoid-scientific-notation" falsevalue="" |
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93 label="Avoid scientific notation in any newly computed columns" |
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94 help="If yes, use fully expanded decimal representation when writing new columns with floating point values. To prevent scientific notation in just specific new columns, you can use numpy's format_float_positional function in the corresponding expression." /> |
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95 <section name="error_handling" title="Error handling"> |
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96 <param name="auto_col_types" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Autodetect column types" |
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97 help="By default, try to use the column types that Galaxy has recorded for the input. This simplifies expressions, but can occasionally cause problems on its own. If disabled all column values are assumed to be strings and you will have to handle conversions to different types explicitly in the expression." /> |
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98 <param argument="--fail-on-non-existent-columns" type="boolean" truevalue="--fail-on-non-existent-columns" falsevalue="" checked="true" label="Fail on references to non-existent columns" |
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99 help="If any expression references a column number that does not exist when that expression gets computed, the tool run will fail. Uncheck to have such a situation handled as a case of a non-computable expression as configured below." /> |
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100 <conditional name="non_computable"> |
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101 <param name="action" type="select" label="If an expression cannot be computed for a row"> |
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102 <option value="--fail-on-non-computable">Fail the entire tool run</option> |
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103 <option value="--skip-non-computable">Skip the row</option> |
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104 <option value="--keep-non-computable">Keep the row unchanged</option> |
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105 <option value="--non-computable-blank">Produce an empty column value for the row</option> |
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106 <option value="--non-computable-default">Fill in a replacement value</option> |
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107 </param> |
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108 <when value="--fail-on-non-computable" /> |
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109 <when value="--skip-non-computable" /> |
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110 <when value="--keep-non-computable" /> |
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111 <when value="--non-computable-blank" /> |
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112 <when value="--non-computable-default"> |
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113 <param name="default_value" type="text" label="Replacement value" help="Pick from suggestions or enter your own."> |
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114 <option value="nan">nan (not a number)</option> |
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115 <option value="inf">inf (infinity)</option> |
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116 <option value="-inf">-inf (negative infinity)</option> |
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117 <option value="NA">NA (not available)</option> |
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118 <option value=".">.</option> |
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119 </param> |
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120 </when> |
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121 </conditional> |
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122 </section> |
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123 </inputs> |
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124 <outputs> |
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125 <data name="out_file1" format_source="input" metadata_source="input"/> |
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126 </outputs> |
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127 <tests> |
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128 <test> |
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129 <param name="cond" value="float(c3-c2)"/> |
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130 <param name="input" value="1.bed" ftype="bed" /> |
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131 <output name="out_file1" file="column_maker_out1.interval"/> |
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132 </test> |
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133 <test> |
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134 <param name="cond" value="c4*1."/> |
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135 <param name="input" value="1.interval" ftype="interval" /> |
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136 <output name="out_file1" file="column_maker_out2.interval"/> |
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137 </test> |
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138 <test> |
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139 <param name="cond" value="c4*1."/> |
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140 <param name="input" value="1.header.tsv" ftype="tabular" /> |
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141 <param name="header_lines_select" value="yes" /> |
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142 <param name="new_column_name" value="value1_again" /> |
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143 <output name="out_file1" file="column_maker_out2.header.tsv"/> |
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144 </test> |
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145 <test> |
9
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146 <param name="cond" value="round(c4*1)"/> |
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147 <param name="input" value="1.interval"/> |
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148 <output name="out_file1" file="column_maker_out3.interval"/> |
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149 </test> |
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150 <test> |
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151 <!-- test that single column input works --> |
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152 <param name="cond" value="c1/10"/> |
9
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153 <param name="input" value="1.tab" ftype="tabular" /> |
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154 <output name="out_file1" file="column_maker_out4.tab"/> |
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155 </test> |
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156 <test> |
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157 <param name="cond" value="float(.0000000000001)"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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158 <param name="input" value="1.bed"/> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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159 <output name="out_file1"> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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160 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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161 <has_text text="CCDS10397" /> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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162 <has_text text="1e-13" /> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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163 </assert_contents> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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164 </output> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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165 </test> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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166 <test> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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167 <param name="cond" value="float(.0000000000001)"/> |
9
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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168 <param name="input" value="1.bed" ftype="bed" /> |
6
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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169 <param name="avoid_scientific_notation" value="true"/> |
5
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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170 <output name="out_file1"> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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171 <assert_contents> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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172 <has_text text="CCDS10397" /> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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173 <has_text text=".0000000000001" /> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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174 <not_has_text text="1e-13" /> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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175 </assert_contents> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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176 </output> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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177 </test> |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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178 <test> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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179 <param name="input" value="1.tab" ftype="tabular" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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180 <repeat name="expressions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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181 <param name="cond" value="c1/10" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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182 <conditional name="add_column"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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183 <param name="mode" value="R" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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184 <param name="pos" value="1" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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185 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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186 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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187 <repeat name="expressions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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188 <param name="cond" value="round(c1*10)" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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189 <conditional name="add_column"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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190 <param name="mode" value="I" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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191 <param name="pos" value="1" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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192 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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193 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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194 <output name="out_file1" file="column_maker_out4.tab" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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195 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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196 <!-- Test list column type in input --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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197 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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198 <param name="input" value="bed12.bed" ftype="bed12" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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199 <!-- get largest blocksize from column 11 of bed12 and use it as |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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200 new score value --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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201 <param name="cond" value="max(map(int, c11))" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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202 <conditional name="add_column"> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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203 <param name="mode" value="R" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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204 <param name="pos" value="5" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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205 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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206 <output name="out_file1" file="bed12_modified.bed" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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207 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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208 <!-- Test error handling example from help section --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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209 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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210 <param name="input" value="short_line_test.tab" ftype="tabular" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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211 <param name="cond" value="c6" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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212 <conditional name="add_column"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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213 <param name="mode" value="R" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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214 <param name="pos" value="6" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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215 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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216 <param name="fail_on_non_existent_columns" value="false" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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217 <param name="action" value="--non-computable-default" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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218 <param name="default_value" value="." /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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219 <output name="out_file1" file="short_line_test_out.tab" /> |
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220 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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221 <!-- Test athletes BMI calculation in presence of NA values as in |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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222 https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html#exercises-4 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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223 --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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224 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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225 <param name="input" value="olympics.tsv" ftype="tabular" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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226 <param name="header_lines_select" value="yes" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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227 <param name="new_column_name" value="BMI" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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228 <param name="cond" value="int(c8) / (int(c7) * int(c7)) * 10000" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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229 <param name="auto_col_types" value="false" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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230 <param name="action" value="--non-computable-default" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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231 <param name="default_value" value="NA" /> |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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232 <output name="out_file1" file="olympics_bmi_out.tab" /> |
6595517c2dd8
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233 </test> |
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iuc
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234 <!-- Test operation used by iwc SARS-CoV-2 consensus building WF that |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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235 turns a 3-column CHROM POS REF tabular dataset into a 3-column BED |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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236 dataset. --> |
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237 <test> |
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iuc
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238 <param name="input" value="chrom_pos_ref.tab" ftype="tabular" /> |
6595517c2dd8
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239 <repeat name="expressions"> |
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240 <param name="cond" value="int(c2) - (len(c3) == 1)" /> |
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241 <conditional name="add_column"> |
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242 <param name="mode" value="R" /> |
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243 <param name="pos" value="2" /> |
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244 </conditional> |
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245 </repeat> |
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246 <repeat name="expressions"> |
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247 <param name="cond" value="int(c2) + ((len(c3) - 1) or 1)" /> |
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248 <conditional name="add_column"> |
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249 <param name="mode" value="R" /> |
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250 <param name="pos" value="3" /> |
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251 </conditional> |
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252 </repeat> |
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253 <output name="out_file1" file="bed_from_chrom_pos_ref.bed" /> |
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254 </test> |
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255 <!-- Test failure on expression syntax errors --> |
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256 <test expect_failure="true"> |
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257 <param name="cond" value="c3- = c2"/> |
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258 <param name="input" value="1.bed" ftype="bed" /> |
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259 <assert_stderr> |
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260 <has_text text="syntax error during parsing." /> |
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261 </assert_stderr> |
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262 </test> |
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263 <!-- Test failure on expression NameErrors --> |
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264 <test expect_failure="true"> |
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265 <param name="cond" value="floatfloat(c3-c2)"/> |
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266 <param name="input" value="1.bed" ftype="bed" /> |
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267 <assert_stderr> |
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268 <has_text text="name 'floatfloat' is not defined" /> |
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269 </assert_stderr> |
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270 </test> |
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271 <!-- Test failure on non-existent column ref --> |
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272 <test expect_failure="true"> |
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273 <param name="cond" value="c7 - c2"/> |
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274 <param name="input" value="1.bed" ftype="bed" /> |
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275 <assert_stderr> |
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276 <has_text text="name 'c7' is not defined" /> |
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277 </assert_stderr> |
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278 </test> |
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279 <!-- Test failure on non-computable expression --> |
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280 <test expect_failure="true"> |
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281 <param name="cond" value="c3 / 0"/> |
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282 <param name="input" value="1.bed" ftype="bed" /> |
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283 <assert_stderr> |
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284 <has_text text="division by zero" /> |
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285 </assert_stderr> |
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286 </test> |
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287 <!-- Test keep-non-computable prevents failure --> |
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288 <test> |
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289 <param name="cond" value="c3 / 0"/> |
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290 <param name="input" value="1.bed" ftype="bed" /> |
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291 <param name="action" value="--keep-non-computable" /> |
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292 <output name="out_file1" file="1.bed" /> |
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293 </test> |
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294 </tests> |
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295 <help><![CDATA[ |
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296 .. class:: infomark |
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297 |
7
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298 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* |
5
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299 |
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300 ----- |
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301 |
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302 **What it does** |
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303 |
9
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304 This tool computes an expression on every row of a dataset and appends or inserts the result as a new column (field). |
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305 |
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306 Several expressions can be specified and will be applied sequentially to each row. |
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307 |
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308 **Expression rules** |
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309 |
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310 - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file |
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311 |
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312 - The following built-in Python functions are available for use in expressions:: |
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313 |
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314 abs | all | any | ascii | bin | bool | chr | ceil | complex | divmod |
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315 |
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316 exp | float | floor | format | hex | int | len | list | log | log10 |
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317 |
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318 list | map | max | min | oct | ord | pow | range | reversed |
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319 |
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320 round | set | sorted | sqrt | str | sum | type |
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321 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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322 - In addition the numpy function ``format_float_positional`` is available to |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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323 control the formatting of floating point numbers. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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324 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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325 - Expressions can be chained, and the tool will keep track of newly added |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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326 columns while working through the chain. This means you can reference a column |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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327 that was created as the result of a previous expression in later ones. |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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328 |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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329 ----- |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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330 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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331 **Simple examples** |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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332 |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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333 If this is your input:: |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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334 |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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335 chr1 151077881 151077918 2 200 - |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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336 chr1 151081985 151082078 3 500 + |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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337 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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338 computing "c4 * c5" will produce:: |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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339 |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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340 chr1 151077881 151077918 2 200 - 400 |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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341 chr1 151081985 151082078 3 500 + 1500 |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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342 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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343 You can also use this tool to evaluate expressions. |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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344 For example, computing "c3 >= c2" for the input above will result in the following:: |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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345 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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346 chr1 151077881 151077918 2 200 - True |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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347 chr1 151081985 151082078 3 500 + True |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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348 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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349 Similarly, computing "type(c2) == type(c3) will return:: |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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350 |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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351 chr1 151077881 151077918 2 200 - True |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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352 chr1 151081985 151082078 3 500 + True |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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353 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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354 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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355 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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356 **Error handling** |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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357 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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358 The tool will always fail on syntax errors in and other unrecoverable parsing |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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359 errors with any of your expressions. For other problems, however, it offers |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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|
360 control over how they should be handled: |
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9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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361 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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362 1. The default for "Autodetect column types" is "Yes", which means the tool |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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363 will evaluate each column value as the type that Galaxy assumes for the |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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364 column. This default behavior will allow you to write simpler expressions. |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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365 The arithmetic expression "c4 * c5" from the first simple example, |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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366 for instance, works only because Galaxy realizes that c4 and c5 are integer |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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367 columns. Occasionally, this autodetection can cause issues. A common |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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368 such situation are missing values in columns that Galaxy thinks are of |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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369 numeric type. If you're getting errors like "Failed to convert some of the |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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370 columns in line #X ...", a solution might be to turn off column type |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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371 autodetection. The price you will have to pay for doing so is that now you |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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372 will have to handle type conversions yourself. In the first example you would |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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373 now have to use the epression: "int(c4) * int(c5)". |
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9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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374 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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375 2. By default, if any expression references columns that are not existing before |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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376 that expression gets computed, the tool will fail, but you can uncheck the |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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377 "Fail on references to non-existent columns" option. If you do so, the result |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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378 will depend on your choice for "If an expression cannot be computed for a row" |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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379 (see 3.) |
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9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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380 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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381 3. The default for rows, for which an expression fails to compute is, again, to |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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382 fail the tool run, but you can also choose to: |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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383 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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384 - skip the row on output |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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385 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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386 This is a simple way to only keep lines conforming to an expected standard. |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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387 It is also easy to mask problems with your expressions with this option so |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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388 take a look at the results and try to understand what gets skipped and for |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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389 what reasons (the stdout of the tool will contain information about both). |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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390 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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391 - keep the row unchanged |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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392 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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393 This can be a good solution if your input contains special separator lines |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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394 that don't follow the general tabular format of other lines and you would |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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395 like to keep those lines |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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396 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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397 - produce an empty column value for the row |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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398 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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399 This will use the empty string as a substitute for non-computable items. |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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400 Different from the "keep the row unchanged option" the problematic line will |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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401 have a column added or changed. This option is a good choice for inputs |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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402 in which all rows have the same tabular layout where you want to make sure |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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403 that the same is true for the output, i.e. that all output lines still have |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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404 the same number of columns. |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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405 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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406 - fill in a replacement value |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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407 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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408 This option is very similar to the previous one, but lets you control the |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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409 replacement value. |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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410 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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411 **Example** |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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412 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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413 In the following input:: |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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414 |
9
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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415 chr1 151077881 151077918 2 200 - |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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416 chr1 151081985 151082078 3 500 + |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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417 chr1 151090031 151090938 4 700 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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418 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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419 the last line does not have a strand column. This violates the bed file format |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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420 specification, which says that unknown strand is to be encoded as ``.`` in the |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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421 strand column. |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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422 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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423 You can fix the file with the following tool run: |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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424 |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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425 **Add expression**: `c6` |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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426 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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427 **Mode of the operation**: `Replace` |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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428 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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429 **Use new column to replace column number**: `6` |
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9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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430 |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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431 **Fail on references to non-existent columns**: `No` |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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432 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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433 **If an expression cannot be computed for a row**: `Fill in a replacement value` |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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434 |
6595517c2dd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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435 **Replacement value**: `.` |
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427903d47026
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
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436 ]]></help> |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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437 <citations /> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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438 </tool> |