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comparison baseline.xml @ 8:525b58fc8622 draft

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author davidvanzessen
date Tue, 02 Jun 2015 05:02:23 -0400
parents 1726dc8f3e0a
children d2b9dd23d944
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7:45a5e3bd9df4 8:525b58fc8622
44 </param> 44 </param>
45 <param name="fixindels" type="select" label="Fix Indels"> 45 <param name="fixindels" type="select" label="Fix Indels">
46 <option value="0">Do Nothing</option> 46 <option value="0">Do Nothing</option>
47 <option value="1">Try and fix Indels</option> 47 <option value="1">Try and fix Indels</option>
48 </param> 48 </param>
49 <param name="boundaries" type="select" label="FWR/CDR3 Boundaries"> 49 <param name="boundaries" type="text" value="1:26:38:55:65:104:116" size="40" label="Custom Boundaries (FWR1Start:FWR1End:CDR1End:FWR2End:CDR3End:FWR3End:CDR3End)" />
50 <option value="1:26:38:55:65:104:-">IMGT® No CDR3</option>
51 <option value="1:26:38:55:65:104:116">IMGT®</option>
52 </param>
53 <param name="selection" type="select" label="Unique Selection Definition"> 50 <param name="selection" type="select" label="Unique Selection Definition">
54 <option value="VGene,AA.JUNCTION">VGene, AA CDR3</option> 51 <option value="VGene,AA.JUNCTION">VGene, AA CDR3</option>
55 <option value="VGene,JGene,AA.JUNCTION">VGene, JGene, AA CDR3</option> 52 <option value="VGene,JGene,AA.JUNCTION">VGene, JGene, AA CDR3</option>
56 <option value="VGene,DGene,JGene,AA.JUNCTION">VGene, DGene, JGene, AA CDR3</option> 53 <option value="VGene,DGene,JGene,AA.JUNCTION">VGene, DGene, JGene, AA CDR3</option>
57 <option value="Sequence.ID">None</option> 54 <option value="Sequence.ID">None</option>
62 </outputs> 59 </outputs>
63 <help> 60 <help>
64 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27. 61 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.
65 62
66 Mohamed Uduman; Gur Yaari; Uri Hershberg; Mark J. Shlomchik; Steven H. Kleinstein. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504. 63 Mohamed Uduman; Gur Yaari; Uri Hershberg; Mark J. Shlomchik; Steven H. Kleinstein. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504.
64
65 **Boundaries**
66
67 IMGT® No CDR3: "1:26:38:55:65:104:-"
68
69 IMGT®: "1:26:38:55:65:104:116"
67 70
68 </help> 71 </help>
69 </tool> 72 </tool>