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annotate column_maker.xml @ 2:292c605c2dc7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 18:52:53 -0500
parents d3f10c90fc96
children 35937a6b04fb
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1 <tool id="Add_a_column1" name="Compute" version="1.1.0">
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2 <description>an expression on every row</description>
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3 <command interpreter="python">
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4 column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}"
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5 </command>
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6 <inputs>
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7 <param name="cond" type="text" value="c3-c2" label="Add expression"/>
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8 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
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9 <param name="round" type="select" label="Round result?">
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10 <option value="no">NO</option>
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11 <option value="yes">YES</option>
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12 </param>
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13 </inputs>
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14 <outputs>
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15 <data format="input" name="out_file1" metadata_source="input"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="cond" value="c3-c2"/>
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20 <param name="input" value="1.bed"/>
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21 <param name="round" value="no"/>
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22 <output name="out_file1" file="column_maker_out1.interval"/>
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23 </test>
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24 <test>
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25 <param name="cond" value="c4*1"/>
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26 <param name="input" value="1.interval"/>
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27 <param name="round" value="no"/>
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28 <output name="out_file1" file="column_maker_out2.interval"/>
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29 </test>
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30 <test>
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31 <param name="cond" value="c4*1"/>
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32 <param name="input" value="1.interval"/>
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33 <param name="round" value="yes"/>
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34 <output name="out_file1" file="column_maker_out3.interval"/>
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35 </test>
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36 </tests>
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37 <help>
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38
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39 .. class:: infomark
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40
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41 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
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42
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43 -----
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44
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45 **What it does**
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46
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47 This tool computes an expression for every row of a dataset and appends the result as a new column (field).
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48
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49 - 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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50
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51 - **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position
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52
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53 -----
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54
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55 **Example**
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56
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57 If this is your input::
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58
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59 chr1 151077881 151077918 2 200 -
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60 chr1 151081985 151082078 3 500 +
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61
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62 computing "c4*c5" will produce::
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63
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64 chr1 151077881 151077918 2 200 - 400.0
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65 chr1 151081985 151082078 3 500 + 1500.0
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66
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67 if, at the same time, "Round result?" is set to **YES** results will look like this::
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68
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69 chr1 151077881 151077918 2 200 - 400
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70 chr1 151081985 151082078 3 500 + 1500
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71
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72 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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73
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74 chr1 151077881 151077918 2 200 - True
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75 chr1 151081985 151082078 3 500 + True
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76
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77 or computing "type(c2)==type('') for Input will return::
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78
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79 chr1 151077881 151077918 2 200 - False
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80 chr1 151081985 151082078 3 500 + False
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81
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83 The following build-in functions are available::
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85 abs | all | any | bin | bool | chr | ceil | cmp | complex
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87 divmod | exp | float | log | floor | hex | int | len | long
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89 max | min | oct | ord | pow | range | reversed
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91 round | sorted | sqrt | str | sum | type | unichr | unicode |
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93 </help>
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94 </tool>