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annotate carpet-src-1/tools/CARPET/genecentrico.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="BECorrelation" name="BEC" version="1.0.0">
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2 <description>Binding-Expression-Correlation</description>
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3 <command interpreter="perl">genecentrico.pl $expr $chip_gff ${prom_choice.prom_start} ${prom_choice.type} $result $output ${prom_choice.prom_end}</command>
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4 <inputs>
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5 <param format="tabular" name="expr" type="data" label="expression file"/>
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6 <param format="bed" name="chip_gff" type="data" label="ChIP on chip GFF results"/>
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7 <conditional name="prom_choice">
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8 <param name="type" type="select" label="Analysis type">
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9 <option value="promoter">only promoter</option>
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10 <option value="all">all gene</option>
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11 </param>
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12 <when value="promoter">
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13 <param name="prom_start" type="integer" size="10" value="-2000" label="Promoter start"/>
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14 <param name="prom_end" type="integer" size="10" value="1000" label="Promoter end"/>
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15 </when>
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16 <when value="all">
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17 <param name="prom_start" type="integer" size="10" value="-2000" label="Promoter start"/>
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18 <param name="prom_end" type="text" size="12" value="NOT-NEEDED" label="Promoter end"/>
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19 </when>
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20 </conditional>
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21 <param name="result" type="select" label="result output">
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22 <option value="number"># of matches</option>
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23 <option value="max_value">max value</option>
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data format="tabular" name="output" />
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28 </outputs>
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29 <help>
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30 .. class:: infomark
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31
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32 **What it does**
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33
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34 BEC integrates the results of expression analysis and ChIP-chip analysis. For each transcript the number of peaks matching in the promoter and/or within the gene body is calculated.
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35
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36 PLEASE, for more detailed information refer to the CARPET user Manual:
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37 click to download_ it.
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38
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39 .. _download: /static/example_file/CARPET_userManual.zip
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40
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41 -----
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42
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43 **Parameters:**
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44
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45 - **Analysis type:**
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46 - **promoter:** only the peaks matching in the promoter region (defined by user) are associated with the transcript
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47 - **all gene:** peaks matching in the promoter and within the gene body are associated with the transcript
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48 - **result output:**
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49 - **# of matches:** the number of matching peaks are reported
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50 - **max value:** the highest score among all matching peaks is reported
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51
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52 --------
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53
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54 .. class:: warningmark
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55
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56 If a peak matches with more than one transcript, it is associated with both.
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57
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58 -----
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59
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60 **INPUT FILES**
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61
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62 - Expression file: file created by TEA
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63 - ChIP on chip GFF results: file create by PeakPicker (or any GFF file)
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64
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65 **OUTPUT FILES**
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66
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67 .. image:: static/images/CARPET/bec_output.png
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68
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69 .. class:: infomark
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70
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71 This results table can be used again as input expression file, to add another ChIP-chip experiment.
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72
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73 </help>
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74
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75 </tool>