Mercurial > repos > devteam > column_maker
annotate column_maker.xml @ 8:02026300aa45 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
author | iuc |
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date | Tue, 09 Mar 2021 18:33:10 +0000 |
parents | 427903d47026 |
children | 6595517c2dd8 |
rev | line source |
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7
427903d47026
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
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1 <tool id="Add_a_column1" name="Compute" version="1.6"> |
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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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2 <description>an expression on every row</description> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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3 <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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4 <requirement type="package" version="3.8">python</requirement> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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5 <requirement type="package" version="1.19.1">numpy</requirement> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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6 </requirements> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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7 <command detect_errors="aggressive"><![CDATA[ |
8
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
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8 ## inject colums and column_types metadata into inputs json |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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9 #import json |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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10 #set inputs_dict = json.load(open($inputs)) |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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11 #set inputs_dict['columns'] = $input.metadata.columns |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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12 #set inputs_dict['column_types'] = $input.metadata.column_types |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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13 ## flatten conditional |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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14 #if $header_lines_conditional.header_lines_select == "yes": |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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15 #set inputs_dict['header_new_column_name'] = str($header_lines_conditional.header_new_column_name) |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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16 #end if |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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17 #set x = json.dump($inputs_dict, open($inputs, 'w')) |
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9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
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18 |
8
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
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19 python '$__tool_directory__/column_maker.py' |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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20 '$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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21 '$out_file1' |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
parents:
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22 --load_json '$inputs' |
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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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23 ]]></command> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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24 <configfiles> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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25 <inputs name="inputs"/> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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26 </configfiles> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents:
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27 <inputs> |
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13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
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28 <param name="cond" type="text" value="c3-c2" label="Add expression"> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
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29 <sanitizer> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
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30 <valid initial="default"> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
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31 <add value="<" /> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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32 <add value=">" /> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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33 <add value=""" /> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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34 <add value="'" /> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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35 </valid> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
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36 </sanitizer> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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37 </param> |
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02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
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38 <param name="input" type="data" format="tabular" label="as a new column to" help="Dataset missing? See TIP below"/> |
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13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
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39 <param name="round" type="boolean" truevalue="yes" falsevalue="no" label="Round result?" /> |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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40 <param name="avoid_scientific_notation" type="boolean" truevalue="yes" falsevalue="no" |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
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41 label="Avoid scientific notation" |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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42 help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers)." /> |
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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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43 <conditional name="header_lines_conditional"> |
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13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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44 <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"
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45 label="Input has a header line with column names?" |
13b6f0007d9e
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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46 help="Select Yes to be able to specify a name for the new column and have it 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." > |
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02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
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47 <option value="no">No</option> |
02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
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48 <option value="yes">Yes</option> |
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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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49 </param> |
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02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
iuc
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50 <when value="no" /> |
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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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51 <when value="yes"> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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52 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" /> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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53 </when> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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54 </conditional> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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55 </inputs> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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56 <outputs> |
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02026300aa45
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
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57 <data name="out_file1" format_source="input" metadata_source="input"/> |
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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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58 </outputs> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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59 <tests> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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60 <test> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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61 <param name="cond" value="c3-c2"/> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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62 <param name="input" value="1.bed"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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63 <param name="round" value="false"/> |
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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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64 <output name="out_file1" file="column_maker_out1.interval"/> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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65 </test> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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66 <test> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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67 <param name="cond" value="c4*1"/> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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68 <param name="input" value="1.interval"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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69 <param name="round" value="false"/> |
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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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70 <output name="out_file1" file="column_maker_out2.interval"/> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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71 </test> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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72 <test> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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73 <param name="cond" value="c4*1"/> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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74 <param name="input" value="1.header.tsv"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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75 <param name="round" value="false"/> |
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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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76 <conditional name="header_lines_conditional"> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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77 <param name="header_lines_select" value="yes" /> |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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78 <param name="header_new_column_name" value="value1_again" /> |
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79 </conditional> |
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80 <output name="out_file1" file="column_maker_out2.header.tsv"/> |
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81 </test> |
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82 <test> |
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83 <param name="cond" value="c4*1"/> |
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84 <param name="input" value="1.interval"/> |
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85 <param name="round" value="true"/> |
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86 <output name="out_file1" file="column_maker_out3.interval"/> |
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87 </test> |
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88 <test> |
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89 <!-- test that single column input works --> |
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90 <param name="cond" value="c1/10"/> |
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91 <param name="input" value="1.tab" ftype="tabular"/> |
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92 <param name="round" value="no"/> |
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93 <output name="out_file1" file="column_maker_out4.tab"/> |
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94 </test> |
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95 <test> |
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96 <param name="cond" value="float(.0000000000001)"/> |
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97 <param name="input" value="1.bed"/> |
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98 <param name="round" value="false"/> |
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99 <output name="out_file1"> |
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100 <assert_contents> |
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101 <has_text text="CCDS10397" /> |
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102 <has_text text="1e-13" /> |
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103 </assert_contents> |
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104 </output> |
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105 </test> |
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106 <test> |
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107 <param name="cond" value="float(.0000000000001)"/> |
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108 <param name="input" value="1.bed"/> |
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109 <param name="round" value="false"/> |
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110 <param name="avoid_scientific_notation" value="true"/> |
5
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111 <output name="out_file1"> |
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112 <assert_contents> |
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113 <has_text text="CCDS10397" /> |
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114 <has_text text=".0000000000001" /> |
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115 <not_has_text text="1e-13" /> |
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116 </assert_contents> |
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117 </output> |
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118 </test> |
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119 </tests> |
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120 <help><![CDATA[ |
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121 .. class:: infomark |
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122 |
7
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123 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* |
5
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124 |
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125 ----- |
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126 |
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127 **What it does** |
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128 |
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129 This tool computes an expression for every row of a dataset and appends the result as a new column (field). |
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130 |
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131 - 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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132 |
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133 - **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position |
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134 |
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135 ----- |
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136 |
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137 **Example** |
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138 |
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139 If this is your input:: |
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140 |
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141 chr1 151077881 151077918 2 200 - |
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142 chr1 151081985 151082078 3 500 + |
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143 |
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144 computing "c4*c5" will produce:: |
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145 |
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146 chr1 151077881 151077918 2 200 - 400.0 |
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147 chr1 151081985 151082078 3 500 + 1500.0 |
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148 |
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149 if, at the same time, "Round result?" is set to **YES** results will look like this:: |
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150 |
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151 chr1 151077881 151077918 2 200 - 400 |
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152 chr1 151081985 151082078 3 500 + 1500 |
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153 |
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154 You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following:: |
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155 |
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156 chr1 151077881 151077918 2 200 - True |
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157 chr1 151081985 151082078 3 500 + True |
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158 |
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159 or computing "type(c2)==type('') for Input will return:: |
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160 |
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161 chr1 151077881 151077918 2 200 - False |
9cd341095afd
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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162 chr1 151081985 151082078 3 500 + False |
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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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163 |
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164 |
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165 The following built-in functions are available:: |
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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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166 |
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167 abs | all | any | bin | bool | chr | ceil | cmp | complex |
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168 |
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169 divmod | exp | float | log | log10 | floor | hex | int | len | long |
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170 |
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171 max | min | oct | ord | pow | range | reversed |
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172 |
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173 round | sorted | sqrt | str | sum | type | unichr | unicode | |
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174 |
7
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175 ]]></help> |
5
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176 <citations /> |
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177 </tool> |