Mercurial > repos > matces > carpet_toolsuite
comparison carpet-src-1/tools/CARPET/Raw_data.xml @ 0:cdd489d98766
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | matces |
|---|---|
| date | Tue, 07 Jun 2011 16:50:41 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:cdd489d98766 |
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| 1 <tool id="view_chip" name="ChipView" version="1.0.0"> | |
| 2 <description>looking into the chip</description> | |
| 3 <command interpreter="python">Raw_data.py $input $output $numerical_column_PM $numerical_column_x $numerical_column_y $title</command> | |
| 4 <inputs> | |
| 5 <param format="tabular" name="input" type="data" label="Source file (*.pair file)"/> | |
| 6 <param name="numerical_column_PM" type="data_column" data_ref="input" numerical="False" value="c10" label="Numerical column for PM" /> | |
| 7 <param name="numerical_column_x" type="data_column" data_ref="input" numerical="False" value="c6" label="Numerical column for x axis" /> | |
| 8 <param name="numerical_column_y" type="data_column" data_ref="input" numerical="False" value="c7" label="Numerical column for y axis" /> | |
| 9 <param name="title" type="text" size="30" value="Image" label="Plot title"/> | |
| 10 </inputs> | |
| 11 <outputs> | |
| 12 <data format="pdf" name="output" /> | |
| 13 </outputs> | |
| 14 <help> | |
| 15 .. class:: infomark | |
| 16 | |
| 17 **What it does** | |
| 18 | |
| 19 This tool creates the image of the array to make sure that no artifacts are present on the surface. | |
| 20 | |
| 21 PLEASE, for more detailed information refer to the CARPET user Manual: | |
| 22 click to download_ it. | |
| 23 | |
| 24 .. _download: /static/example_file/CARPET_userManual.zip | |
| 25 | |
| 26 ----- | |
| 27 | |
| 28 .. class:: warningmark | |
| 29 | |
| 30 This tool requires at least three numerical column **"X position"**, **"Y position"** (the position coordinates on the chip of each probe) and **"PM value"** (the raw signal of each probe). | |
| 31 | |
| 32 ----- | |
| 33 | |
| 34 **Example** | |
| 35 | |
| 36 - On **Get Data** section it is possible to upload your files clicking on **"Upload File from your computer"**. | |
| 37 | |
| 38 Click here_ to download a pair_file example. | |
| 39 | |
| 40 .. _here: /static/example_file/Pair_file.txt.zip | |
| 41 | |
| 42 - Input dataset pair_file from NimbleGen contained all these informations (eleven columns: c1, c2, c3, c4, c5... c11):: | |
| 43 | |
| 44 c1 c2 c3 c4 c5 c6 c7 c8 c9 c10 c11 | |
| 45 IMAGE_ID GENE_EXPR_OPTION SEQ_ID PROBE_ID POSITION X Y MATCH_INDEX SEQ_URL PM MM | |
| 46 1251702_635 FORWARD CHR19 CHR1900P000011001 11001 565 381 64160375 ____ 5459.89 0.00 | |
| 47 1251702_635 FORWARD CHR19 CHR1900P000011050 11050 610 656 64160376 ____ 865.75 0.00 | |
| 48 | |
| 49 | |
| 50 - Chose column **c10** for "PM value", **c6** for "X position" and **c7** for "Y position". | |
| 51 | |
| 52 | |
| 53 | |
| 54 .. image:: static/images/CARPET/chip.jpg | |
| 55 | |
| 56 </help> | |
| 57 </tool> | |
| 58 |