Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/common_unique_probe.xml @ 1:78770028dcf1 default tip

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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:59:33 -0400
parents cdd489d98766
children
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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="common unique" name="Com&amp;Uni" version="1.1.0">
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2 <description>easy way to compare results</description>
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3 <command>/data/galaxy/tools/CARPET/comuni $window ${match_choice.type} ${match_choice.conc} $input1 $input2 $output</command>
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4 <inputs>
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5 <param format="tabular" name="input1" type="data" label="Principal table"/>
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6 <param format="tabular" name="input2" type="data" label="Secondary table"/>
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7 <param name="window" type="integer" size="7" value="0" label="flank"/>
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8 <conditional name="match_choice">
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9 <param name="type" type="select" label="Analysis type">
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10 <option value="common">common</option>
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11 <option value="unique">unique</option>
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12 <option value="union">union</option>
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13 </param>
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14 <when value="common">
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15 <param name="conc" type="select" label="coordinate common">
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16 <option value="yes">merge</option>
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17 <option value="no">Principal table</option>
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18 </param>
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19 </when>
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20 <when value="unique">
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21 <param name="conc" type="select" label="coordinate common">
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22 <option value="no">Principal table</option>
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23 </param>
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24 </when>
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25 <when value="union">
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26 <param name="conc" type="select" label="coordinate common">
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27 <option value="yes">merge</option>
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28 </param>
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29 </when>
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30 </conditional>
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31 </inputs>
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32 <outputs>
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33 <data format="bed" name="output" file="common.dat"/>
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34 </outputs>
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35
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36 <tests>
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37 <test>
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38 <param name="input" value="1.gff"/>
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39 <output name="output" file="wig-gff2bed.dat"/>
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40 </test>
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41 </tests>
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42 <help>
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43 .. class:: infomark
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44
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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45 **What it does**
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46
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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47 This tool evaluates the co-occurence of peaks between two GFF files. Common and/or unique peaks can be sorted out as exemplified below. It is possible to add a flanking region to the coordinates of the original peaks.
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48
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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49 --------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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50
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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51 **Example:**
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52
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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53 - **Common merge**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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54
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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55 .. image:: static/images/CARPET/common_merg.png
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56
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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57 --------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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58
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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59 - **Common Principal table**
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60
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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61 .. image:: static/images/CARPET/common_princ.png
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62
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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63 --------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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64
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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65 - **Unique**
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66
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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67 .. image:: static/images/CARPET/unique.png
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68
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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69 --------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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70
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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71 - **Union**
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72
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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73 .. image:: static/images/CARPET/union.png
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74
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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75 </help>
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76 </tool>