Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/Raw_data.xml @ 0:cdd489d98766

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