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1 <tool id ="pySelectMotifsFromGTF" name="pySelectMotifsFromGTF">
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2 <requirements>
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3 <requirement type="package">pyCRAC</requirement>
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4 </requirements>
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5 <command interpreter="python">
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6 /usr/local/bin/pySelectMotifsFromGTF.py
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7 --gtf $input
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8 -m $motif
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9 -o $out
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10 -l $length
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11 -z $zscore
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12 </command>
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13 <version_command>/usr/local/bin/pySelectMotifsFromGTF.py --version</version_command>
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14 <inputs>
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15 <param format="gtf" name="input" type="data" label="Input File -f" help="pyMotif gtf output files" />
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16 <param format="txt" name="motif" type="text" size="200" value="KBCTTG" label="motif string" help="Enter motif (all uppercase) you want to extract from the pyMotif gtf output file">
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17 <validator type="empty_field" />
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18 </param>
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19 <param format="integer" type="integer" value="6" size="5" name="length" label="Length --length" help="Set a Kmer Length. Note that the length has to be at least as long as your k-mer sequence, otherwise the program will not run correctly" />
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20 <param format="float" type="float" value="0" size="5" name="zscore" label="Z Score --Z_score" help="Set a minimum Kmer Z_score" />
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21 <param name="label" type="text" format="txt" size="30" value="pySelectMotifsFromGTF" label="Enter output file label -o" />
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22 </inputs>
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23
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24 <outputs>
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25 <data format="gtf" name="out" label="${label.value}_${motif.value}.gtf"/>
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26 </outputs>
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27 <help>
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28
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29
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30 .. class:: infomark
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31
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32 **pySelectMotifsFromGTF**
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33
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34 pySelectMotifsFromGTF is part of the pyCRAC_ package. Extracts your favourite k-mer sequence from pyMotif GTF output files.
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35 Note that you can include degenerate nucleotides in your motif string::
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36
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37 N = A, G, C or T
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38 R = A or G = puRine
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39 Y = C or T = pYrimidine
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40 M = A or C = aroMatic
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41 S = G or C
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42 W = A or T
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43 K = G or T = Keto
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44 V = A, C or G = Not T (letter after)
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45 D = A, G or T = Not C
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46 H = A, C or T = Not G
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47 B = C, G or T = Not A
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48
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49 So if you enter KBCTTG as search string and length=6, then the program will extract a large number of six-mers from your data.
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50 If you set length = 8, it will look for this pattern in a stretch of 8 nucleotides.
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51
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52 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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53
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54 ------
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55
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56 **Parameter list**
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57
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58 Options::
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59
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60 --gtf=Yourfavoritegtf.gtf
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61 type the path to the gtf file that you want to use. By
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62 default it expects data from the standard input
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63 -o FILE, --output=FILE
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64 Optional.Specify the name of the output file. Default
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65 is standard output. Make sure it has the .gtf
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66 extension!
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67 -m KBCTTG, --motif=KBCTTG
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68 Specify the motif you want extract from the GTF file.
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69 -z 15.0, --Z_score=15.0
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70 Set a minimum k-mer Z-score. Default=0
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71 -l 4, --length=4
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72 Set a k-mer length. Default is no length filtering
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73
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74 </help>
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75 </tool>
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