Mercurial > repos > cafletezbrant > kmersvm
comparison kmersvm/tomtom.xml @ 7:fd740d515502 draft default tip
Uploaded revised kmer-SVM to include modules from kmer-visual.
| author | cafletezbrant |
|---|---|
| date | Sun, 16 Jun 2013 18:06:14 -0400 |
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| 6:1aea7c1a9ab1 | 7:fd740d515502 |
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| 1 <tool id="tomtom" name="Tomtom" version="1.0.0"> | |
| 2 | |
| 3 <description>Tomtom tool for motif searching</description> | |
| 4 <command>/home/galaxy/meme/bin/tomtom -no-ssc -internal -text -verbosity 1 -thresh $thresh | |
| 5 #if str($cut.cut_choice) == 'e.value': | |
| 6 -evalue | |
| 7 #end if | |
| 8 | |
| 9 #if str($dist.dist) == 'ed': | |
| 10 -dist ed | |
| 11 #elif str($dist.dist) == 'sw': | |
| 12 -dist sandelin | |
| 13 #else | |
| 14 -dist pearson | |
| 15 #end if | |
| 16 | |
| 17 $input1 /home/galaxy/meme/db/combined_db.meme > tomtom_out.txt | |
| 18 | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <param format="txt" name="input1" type="data" label="PWM File"/> | |
| 22 <param type="float" value="0.5" label="Threshold" name="thresh"/> | |
| 23 <conditional name="cut"> | |
| 24 <param name="cut_choice" type="select" label="Threshold Type"> | |
| 25 <option value="q.value" selected="true">q-value</option> | |
| 26 <option value="e.value">E-value</option> | |
| 27 </param> | |
| 28 </conditional> | |
| 29 | |
| 30 <conditional name="dist"> | |
| 31 <param name="dist" type="select" label="Distance Metric"> | |
| 32 <option value="pearson" selected="true">Pearson</option> | |
| 33 <option value="ed">Euclidean</option> | |
| 34 <option value="sw">Sandelin-Wasserman Function</option> | |
| 35 </param> | |
| 36 </conditional> | |
| 37 </inputs> | |
| 38 | |
| 39 <outputs> | |
| 40 <data format="txt" name="Tomtom Results" from_work_dir="tomtom_out.txt" label="${tool.name} on ${on_string}: Tomtom Matches"/> | |
| 41 | |
| 42 </outputs> | |
| 43 <help> | |
| 44 | |
| 45 Tomtom is a tool for comparing a DNA motif to a database of known motifs. For an in-depth explanation of the Tomtom software see here_. | |
| 46 | |
| 47 ---- | |
| 48 | |
| 49 **Recommended Settings** | |
| 50 | |
| 51 We recommend most users use the Tomtom defaults of q-value for score, the cutoff of 0.5 and the Pearson correlation coefficent for distance metric. | |
| 52 | |
| 53 ---- | |
| 54 | |
| 55 **Parameters** | |
| 56 | |
| 57 We offer users the options of choosing which distance metric can be used to find matching motifs. Specifically, we offer the Pearson correlation coefficient, the Euclidean distance and the Sandelin-Wasserman Function. | |
| 58 | |
| 59 * The Pearson correlation coefficient measures the similarity between columns of position weight matrices (PWMs). | |
| 60 | |
| 61 * The Euclidean distance can be thought of as the length of the straight line between two PWMs. | |
| 62 | |
| 63 * The Sandelin-Wasserman function sums the column-wise differences between PWMs. | |
| 64 | |
| 65 We also offer the choice of E-value and q-value to threshold the results returned by Tomtom. | |
| 66 | |
| 67 * The E-value controls the expected number of false positives and can be any number. | |
| 68 | |
| 69 * The q-value controls the false discovery rate and is a number between 0 and 1. | |
| 70 | |
| 71 ---- | |
| 72 | |
| 73 Note that at this time we only offer Tomtom output in txt format. | |
| 74 | |
| 75 ---- | |
| 76 | |
| 77 **Citation** | |
| 78 | |
| 79 If you use this tool, please cite: Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007. | |
| 80 | |
| 81 .. _here: http://meme.nbcr.net/meme/tomtom-intro.html | |
| 82 | |
| 83 </help> | |
| 84 </tool> |