Mercurial > repos > chmaramis > irprofiler
comparison test-data/README.html @ 1:acaa8e8a0b88 draft default tip
Uploaded test-data & added tool help
| author | chmaramis |
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| date | Mon, 30 Apr 2018 04:47:52 -0400 |
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| 0:0e37e5b73273 | 1:acaa8e8a0b88 |
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| 1 <!DOCTYPE html> | |
| 2 <html lang="en"> | |
| 3 <head> | |
| 4 <meta charset="utf-8"> | |
| 5 <!--<link rel="stylesheet" href="style/base.css" type="text/css" />--> | |
| 6 </head> | |
| 7 <body style="margin-left: 1cm"> | |
| 8 <div class="jumbotron"> | |
| 9 <div class="container"> | |
| 10 <h3>Test Data Name Conventions</h3> | |
| 11 <p>Concerning the naming of the execution parameters, input and output files, the following convention applies: </p> | |
| 12 <ul> | |
| 13 <li class="container">The name starts with the tool specifier; see Tool Specifiers Table below.</li> | |
| 14 <li class="container">The clonotype definition specifier follows, if needed; see Clonotype Definition Specifiers Table below.</li> | |
| 15 <li class="container">The gene specifier (geneV or geneJ) follows, if needed.</li> | |
| 16 <li class="container">The cell type specifier (BCR or TCR) follows.</li> | |
| 17 <li class="container">The name ends with the file content specifier (input, output or parameters).</li> | |
| 18 </ul> | |
| 19 | |
| 20 <p><i>Tool Specifiers Table</i></p> | |
| 21 <table style="border-spacing: 10px 0px"> | |
| 22 <tr align="left"> | |
| 23 <th>Index</th> | |
| 24 <th>Tool</th> | |
| 25 <th>Specifier</th> | |
| 26 </tr> | |
| 27 <tr> | |
| 28 <td>1</td> | |
| 29 <td>Data Filtering</td> | |
| 30 <td>data_filter</td> | |
| 31 </tr> | |
| 32 <tr> | |
| 33 <td>2</td> | |
| 34 <td>Clonotype Diversity & Expression</td> | |
| 35 <td>clono_compute</td> | |
| 36 </tr> | |
| 37 <tr> | |
| 38 <td>3</td> | |
| 39 <td>Gene Usage</td> | |
| 40 <td>gene_usage</td> | |
| 41 </tr> | |
| 42 <tr> | |
| 43 <td>4</td> | |
| 44 <td>Public Clonotypes</td> | |
| 45 <td>public_clonos</td> | |
| 46 </tr> | |
| 47 <tr> | |
| 48 <td>5</td> | |
| 49 <td>Exclusive Clonotypes</td> | |
| 50 <td>exclusive_clonos</td> | |
| 51 </tr> | |
| 52 <tr> | |
| 53 <td>6</td> | |
| 54 <td>Gene Usage Comparison</td> | |
| 55 <td>gene_compare</td> | |
| 56 </tr> | |
| 57 </table> | |
| 58 | |
| 59 <br> | |
| 60 | |
| 61 <p><i>Clonotype Definition Specifiers Table</i></p> | |
| 62 <table style="border-spacing: 10px 0px"> | |
| 63 <tr align="left"> | |
| 64 <th>Index</th> | |
| 65 <th>Clonotype Definition</th> | |
| 66 <th>Specifier</th> | |
| 67 </tr> | |
| 68 <tr> | |
| 69 <td>1</td> | |
| 70 <td>CDR3</td> | |
| 71 <td>def1</td> | |
| 72 </tr> | |
| 73 <tr> | |
| 74 <td>2</td> | |
| 75 <td>V+CDR3</td> | |
| 76 <td>def2</td> | |
| 77 </tr> | |
| 78 <tr> | |
| 79 <td>3</td> | |
| 80 <td>J+CDR3</td> | |
| 81 <td>def3</td> | |
| 82 </tr> | |
| 83 <tr> | |
| 84 <td>4</td> | |
| 85 <td>V+J+CDR3</td> | |
| 86 <td>def4</td> | |
| 87 </tr> | |
| 88 <tr> | |
| 89 <td>5</td> | |
| 90 <td>V+D+J+CDR3</td> | |
| 91 <td>def5</td> | |
| 92 </tr> | |
| 93 </table> |