Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/annotation_expr.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="Annotation_Expr" name="ENO" version="1.0.0">
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2 <description>Expression NOtator</description>
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3 <command interpreter="perl">annotation_expr_intron.pl $input1 $input2 $output</command>
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4 <inputs>
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5 <param format="tabular" name="input1" type="data" label="Expression file"/>
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6 <param format="tabular" name="input2" type="data" label="Annotation table"/>
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7 </inputs>
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8 <outputs>
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9 <data format="tabular" name="output"/>
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10 </outputs>
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11 <help>
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12 .. class:: infomark
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13
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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14 **What it does**
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16 ENO assigns each exon of a transcript the relative matching probes of the array. If a probe matches with more than one transcript, it is associated to every transcript.
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18 PLEASE, for more detailed information refer to the CARPET user Manual:
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19 click to download_ it.
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21 .. _download: /static/example_file/CARPET_userManual.zip
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23 --------
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25 .. class:: warningmark
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27 **Annotation Table**
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28
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29 Annotation table was directly downloadable from **"Get Data"** section (**"UCSC Main table browser"** link).
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30 Pay attention to choose the right output format (**"all field from selected table"**) and check **"send output to Galaxy"**.
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32 It is possible to download many different annotation tables coming from different organisms and database such as RefSeq, UCSC gene, FlyBase, EST, etc etc...
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34 **All annotation tables must have headers.**
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37 --------
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39 .. class:: warningmark
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41 **Custom annotation table**
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42
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43 .. class:: infomark
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46 **About format**
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47
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48 Annotation table format must be the same downlodable from UCSC. In the specific case of this tool the following fields must be present:
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50 1. **chrom** - The name of the chromosome (e.g. chr1, chrY_random).
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51 2. **chromStart** - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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52 3. **chromEnd** - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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53 4. **name** - The name of the BED line.
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54 5. **strand** - Defines the strand - either + or - .
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55 6. **blockCount** - The number of blocks (exons) in the BED line.
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56 7. **blockSizes** - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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57 8. **blockStarts** - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
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60 The table **must** have headers
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63 ---------
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65 .. class:: infomark
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66
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67 **How does it work?**
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68
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69 .. image:: static/images/CARPET/Eno.png
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73 </help>
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74 </tool>