diff test-data/rif_resistant_variants_report.html @ 3:42818629ec4c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
author iuc
date Fri, 31 May 2024 20:06:49 +0000
parents adc0645b945c
children
line wrap: on
line diff
--- a/test-data/rif_resistant_variants_report.html	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/rif_resistant_variants_report.html	Fri May 31 20:06:49 2024 +0000
@@ -22,10 +22,545 @@
             </h2>
         </div>
                         <hr>
-        <div>
-    <p>No variant data was found for this VCF file. Is it a <a href="http://snpeff.sourceforge.net/SnpEff_manual.html"
-            target="_blank" rel="noreferrer noopener">SnpEff</a> annotated VCF file?</p>
-    <p>Kindly check if the '<strong>ANN</strong>' field is present.</p>
+        <div class="row justify-content-center align-items-center">
+    <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">
+        <thead class="thead-light">
+            <tr>
+                <th scope="col">CHR</th>
+                <th scope="col">GENE</th>
+                <th scope="col">LOCUS</th>
+                <th scope="col">PRODUCT</th>
+                <th scope="col">IS_SNV</th>
+                <th scope="col">EFFECT</th>
+                <th scope="col">POS</th>
+                <th scope="col">REF</th>
+                <th scope="col">ALT</th>
+                <th scope="col">BIOTYPE</th>
+                <th scope="col">NUCLEOTIDE</th>
+                <th scope="col">CONSEQUENCE</th>
+                <th scope="col">IMPACT</th>
+                <th scope="col">PATHWAY</th>
+            </tr>
+        </thead>
+        <tbody>
+
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0014c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0014c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0014c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A15890..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A15890..None"
+                        target="_blank" rel="noreferrer noopener">15890</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.1581C>T</td>
+                <td>p.Ser527Ser</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0127</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0127" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0127</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A154990..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A154990..None"
+                        target="_blank" rel="noreferrer noopener">154990</a>
+                </td>
+                <td>G</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.759G>T</td>
+                <td>p.Arg253Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0284</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0284" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0284</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A346693..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A346693..None"
+                        target="_blank" rel="noreferrer noopener">346693</a>
+                </td>
+                <td>G</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.1059G>T</td>
+                <td>p.Ser353Ser</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0372c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0372c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0372c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A449194..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A449194..None"
+                        target="_blank" rel="noreferrer noopener">449194</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.192C>T</td>
+                <td>p.Gly64Gly</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0411c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0411c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0411c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A497491..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A497491..None"
+                        target="_blank" rel="noreferrer noopener">497491</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.810C>T</td>
+                <td>p.Asp270Asp</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0667</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0667" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0667</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>missense_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A761110..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A761110..None"
+                        target="_blank" rel="noreferrer noopener">761110</a>
+                </td>
+                <td>A</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.1304A>T</td>
+                <td>p.Asp435Val</td>
+                <td>MODERATE</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0715</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0715" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0715</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A811753..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A811753..None"
+                        target="_blank" rel="noreferrer noopener">811753</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.12C>T</td>
+                <td>p.His4His</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv1391</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1391" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv1391</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1565566..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1565566..None"
+                        target="_blank" rel="noreferrer noopener">1565566</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.126C>T</td>
+                <td>p.Pro42Pro</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv1630</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1630" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv1630</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1834177..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1834177..None"
+                        target="_blank" rel="noreferrer noopener">1834177</a>
+                </td>
+                <td>A</td>
+                <td>C</td>
+                <td>protein_coding</td>
+                <td>c.636A>C</td>
+                <td>p.Arg212Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv1640c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1640c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv1640c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1849051..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1849051..None"
+                        target="_blank" rel="noreferrer noopener">1849051</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.2985G>A</td>
+                <td>p.Pro995Pro</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2231c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2231c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2231c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2505085..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2505085..None"
+                        target="_blank" rel="noreferrer noopener">2505085</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.615C>T</td>
+                <td>p.Ala205Ala</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2268c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2268c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2268c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2543395..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2543395..None"
+                        target="_blank" rel="noreferrer noopener">2543395</a>
+                </td>
+                <td>T</td>
+                <td>C</td>
+                <td>protein_coding</td>
+                <td>c.882A>G</td>
+                <td>p.Glu294Glu</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2357c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2357c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2357c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2640807..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2640807..None"
+                        target="_blank" rel="noreferrer noopener">2640807</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.258C>T</td>
+                <td>p.Val86Val</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2472</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2472" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2472</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2775361..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2775361..None"
+                        target="_blank" rel="noreferrer noopener">2775361</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.90C>T</td>
+                <td>p.Arg30Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2483c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2483c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2483c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2789798..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2789798..None"
+                        target="_blank" rel="noreferrer noopener">2789798</a>
+                </td>
+                <td>G</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.1225C>A</td>
+                <td>p.Arg409Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3109</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3109" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3109</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3477942..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3477942..None"
+                        target="_blank" rel="noreferrer noopener">3477942</a>
+                </td>
+                <td>A</td>
+                <td>G</td>
+                <td>protein_coding</td>
+                <td>c.294A>G</td>
+                <td>p.Thr98Thr</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3210c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3210c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3210c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3587446..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3587446..None"
+                        target="_blank" rel="noreferrer noopener">3587446</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.94C>T</td>
+                <td>p.Leu32Leu</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3799c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3799c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254431..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254431..None"
+                        target="_blank" rel="noreferrer noopener">4254431</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.1518C>T</td>
+                <td>p.Asp506Asp</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3799c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3799c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>missense_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254477..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254477..None"
+                        target="_blank" rel="noreferrer noopener">4254477</a>
+                </td>
+                <td>T</td>
+                <td>C</td>
+                <td>protein_coding</td>
+                <td>c.1472A>G</td>
+                <td>p.His491Arg</td>
+                <td>MODERATE</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                    </tbody>
+        <tfoot class="thead-light">
+            <tr>
+                <th scope="col">CHR</th>
+                <th scope="col">GENE</th>
+                <th scope="col">LOCUS</th>
+                <th scope="col">PRODUCT</th>
+                <th scope="col">TYPE</th>
+                <th scope="col">EFFECT</th>
+                <th scope="col">POS</th>
+                <th scope="col">REF</th>
+                <th scope="col">ALT</th>
+                <th scope="col">BIOTYPE</th>
+                <th scope="col">NUCLEOTIDE</th>
+                <th scope="col">CONSEQUENCE</th>
+                <th scope="col">IMPACT</th>
+                <th scope="col">PATHWAY</th>
+            </tr>
+        </tfoot>
+    </table>
+</div>
+</main>
+<div class="mt-5">
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