Mercurial > repos > devteam > column_maker
annotate column_maker.xml @ 1:d3f10c90fc96 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:14:53 -0400 |
| parents | 4dadd821722f |
| children | 292c605c2dc7 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="Add_a_column1" name="Compute" version="1.1.0"> |
| 2 <description>an expression on every row</description> | |
| 3 <command interpreter="python"> | |
| 4 column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}" | |
| 5 </command> | |
| 6 <inputs> | |
|
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d3f10c90fc96
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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7 <param name="cond" type="text" value="c3-c2" label="Add expression"/> |
| 0 | 8 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/> |
| 9 <param name="round" type="select" label="Round result?"> | |
| 10 <option value="no">NO</option> | |
| 11 <option value="yes">YES</option> | |
| 12 </param> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data format="input" name="out_file1" metadata_source="input"/> | |
| 16 </outputs> | |
| 17 <tests> | |
| 18 <test> | |
| 19 <param name="cond" value="c3-c2"/> | |
| 20 <param name="input" value="1.bed"/> | |
| 21 <param name="round" value="no"/> | |
| 22 <output name="out_file1" file="column_maker_out1.interval"/> | |
| 23 </test> | |
| 24 <test> | |
| 25 <param name="cond" value="c4*1"/> | |
| 26 <param name="input" value="1.interval"/> | |
| 27 <param name="round" value="no"/> | |
| 28 <output name="out_file1" file="column_maker_out2.interval"/> | |
| 29 </test> | |
| 30 <test> | |
| 31 <param name="cond" value="c4*1"/> | |
| 32 <param name="input" value="1.interval"/> | |
| 33 <param name="round" value="yes"/> | |
| 34 <output name="out_file1" file="column_maker_out3.interval"/> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 | |
| 39 .. class:: infomark | |
| 40 | |
| 41 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* | |
| 42 | |
| 43 ----- | |
| 44 | |
| 45 **What it does** | |
| 46 | |
| 47 This tool computes an expression for every row of a dataset and appends the result as a new column (field). | |
| 48 | |
| 49 - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file | |
| 50 | |
| 51 - **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position | |
| 52 | |
| 53 ----- | |
| 54 | |
| 55 **Example** | |
| 56 | |
| 57 If this is your input:: | |
| 58 | |
| 59 chr1 151077881 151077918 2 200 - | |
| 60 chr1 151081985 151082078 3 500 + | |
| 61 | |
| 62 computing "c4*c5" will produce:: | |
| 63 | |
| 64 chr1 151077881 151077918 2 200 - 400.0 | |
| 65 chr1 151081985 151082078 3 500 + 1500.0 | |
| 66 | |
| 67 if, at the same time, "Round result?" is set to **YES** results will look like this:: | |
| 68 | |
| 69 chr1 151077881 151077918 2 200 - 400 | |
| 70 chr1 151081985 151082078 3 500 + 1500 | |
| 71 | |
| 72 You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following:: | |
| 73 | |
| 74 chr1 151077881 151077918 2 200 - True | |
| 75 chr1 151081985 151082078 3 500 + True | |
| 76 | |
| 77 or computing "type(c2)==type('') for Input will return:: | |
| 78 | |
| 79 chr1 151077881 151077918 2 200 - False | |
| 80 chr1 151081985 151082078 3 500 + False | |
| 81 | |
| 82 </help> | |
| 83 </tool> |