Mercurial > repos > john-mccallum > pcr_markers

annotate parse_primersearch.xml @ 0:21053f7f9ed1 draft

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First upload of PCR Marker tools
author john-mccallum
date Thu, 14 Jun 2012 19:29:26 -0400
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1 <?xml version="1.0"?>
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2 <tool id="parse_primersearch_1" name="Parse Primer search">
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3 <description>Parse EMBOSS primer search output to tabular </description>
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4 <command interpreter="perl">parse_primersearch.pl $inputPrimersearchFile $outputfile </command>
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5 <inputs>
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6 <param format="primersearch" name="inputPrimersearchFile" type="data" label="Primersearch output file"/>
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7 </inputs>
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8 <outputs>
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9
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10 <data format="tabular" name="outputfile" />
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11 </outputs>
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12 <help>
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13
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14 .. class:: infomark
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15
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16 **TIP**
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17
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18 This tool parses EMBOSS primersearch_ output into columnar format suitable for use as interval
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19
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21
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22 Columns are:
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23
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24 1. Primer set ID
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25 2. Hit ID
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26 3. Number of mismatches
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27 4. Amplimer start
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28 5. Amplimer end
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29 6. Amplicon length
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30
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31
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32 ----
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33
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34 **Example**
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35
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36 *output*
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37
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38 ::
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39
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40 ACP032 isotig07062 0 214 363 149
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41 ACP223 isotig04647 0 362 574 212
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42 ACP224 isotig04647 0 303 519 216
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43 ACP225 isotig04647 0 153 355 202
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44 ACP363 isotig10393 0 93 193 100
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45 ACP394 isotig00271 0 894 986 92
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46 ACP394 isotig00273 0 805 897 92
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47 ACP440 isotig05277 0 506 601 95
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48 ACP615 isotig00271 0 894 978 84
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49 ACP615 isotig00273 0 805 889 84
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50 AJK295 isotig06005 0 182 651 469
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51
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52
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53 .. _primersearch: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html
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54
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55 -----------------------
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56
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57 *If you use this tool please cite:*
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58
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59 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
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60 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
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61 (2012)
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62
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63 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
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64 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
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65
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66
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67 </help>
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68 </tool>