# HG changeset patch
# User iuc
# Date 1625649764 0
# Node ID adc0645b945c7820f865ccc67c226d5147d6236d
# Parent  02d81b994ef59178df771210961456498d8d05a8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"

diff -r 02d81b994ef5 -r adc0645b945c tbvcfreport.xml
--- a/tbvcfreport.xml	Thu Aug 29 08:18:59 2019 -0400
+++ b/tbvcfreport.xml	Wed Jul 07 09:22:44 2021 +0000
@@ -2,7 +2,7 @@
 <tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0">
   <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description>
   <macros>
-    <token name="@TOOL_VERSION@">0.1.7</token>
+    <token name="@TOOL_VERSION@">0.1.8</token>
   </macros>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement>
@@ -86,8 +86,8 @@
     <test>
       <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" />
       <param name="tbprofiler_json" value="rif_resistant.results.json" ftype="json" />
-      <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report.html" ftype="html" />
-      <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report.txt" ftype="txt" />
+      <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report_with_lineage.html" ftype="html" />
+      <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report_with_lineage.txt" ftype="txt" />
       <output name="drug_resistance_report_html" file="rif_resistant_drug_resistance_report.html" lines_diff="2" ftype="html" />
       <output name="drug_resistance_report_txt" compare="diff" lines_diff="2" file="rif_resistant_drug_resistance_report.txt" ftype="txt" />
     </test>
diff -r 02d81b994ef5 -r adc0645b945c test-data/rif_resistant_drug_resistance_report.html
--- a/test-data/rif_resistant_drug_resistance_report.html	Thu Aug 29 08:18:59 2019 -0400
+++ b/test-data/rif_resistant_drug_resistance_report.html	Wed Jul 07 09:22:44 2021 +0000
@@ -21,29 +21,6 @@
                 rif_resistant Report
             </h2>
         </div>
-                <div class="row">
-            <table class="table table-striped table-hover">
-                <caption>Lineage Info</caption>
-                <thead class="thead-light">
-                    <tr>
-                        <th scope="col">Species</th>
-                        <th scope="col">Lineage</th>
-                        <th scope="col">Sub-lineage</th>
-                        <th scope="col">Agreement with SNPs from this lineage</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    <tr>
-                        <td>M. tuberculosis</td>
-                        <td>Lineage 4</td>
-                        <td>
-                                                        Not Available
-                                                    </td>
-                        <td>99%</td>
-                    </tr>
-                </tbody>
-            </table>
-        </div>
                         <hr>
         <div class="row">
     <h3 class="mb-2">
diff -r 02d81b994ef5 -r adc0645b945c test-data/rif_resistant_drug_resistance_report.txt
--- a/test-data/rif_resistant_drug_resistance_report.txt	Thu Aug 29 08:18:59 2019 -0400
+++ b/test-data/rif_resistant_drug_resistance_report.txt	Wed Jul 07 09:22:44 2021 +0000
@@ -1,6 +1,8 @@
 #Rif_resistant Report
-#Species	Lineage	Sub-lineage	Agreement
-M. tuberculosis	Lineage 4		99%
+#Lineage	Family	Spoligotype	RD	Agreement
+lineage2	East-Asian	Beijing	RD105	1.0
+lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207	1.0
+lineage2.2.2	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207	1.0
 
 #TBProfiler Drug Resistance Report
 
diff -r 02d81b994ef5 -r adc0645b945c test-data/rif_resistant_variants_report.html
--- a/test-data/rif_resistant_variants_report.html	Thu Aug 29 08:18:59 2019 -0400
+++ b/test-data/rif_resistant_variants_report.html	Wed Jul 07 09:22:44 2021 +0000
@@ -21,29 +21,6 @@
                 rif_resistant Report
             </h2>
         </div>
-                <div class="row">
-            <table class="table table-striped table-hover">
-                <caption>Lineage Info</caption>
-                <thead class="thead-light">
-                    <tr>
-                        <th scope="col">Species</th>
-                        <th scope="col">Lineage</th>
-                        <th scope="col">Sub-lineage</th>
-                        <th scope="col">Agreement with SNPs from this lineage</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    <tr>
-                        <td>M. tuberculosis</td>
-                        <td>Lineage 4</td>
-                        <td>
-                                                        Not Available
-                                                    </td>
-                        <td>99%</td>
-                    </tr>
-                </tbody>
-            </table>
-        </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"
diff -r 02d81b994ef5 -r adc0645b945c test-data/rif_resistant_variants_report.txt
--- a/test-data/rif_resistant_variants_report.txt	Thu Aug 29 08:18:59 2019 -0400
+++ b/test-data/rif_resistant_variants_report.txt	Wed Jul 07 09:22:44 2021 +0000
@@ -1,5 +1,4 @@
 #Rif_resistant Report
-#Species	Lineage	Sub-lineage	Agreement
-M. tuberculosis	Lineage 4		99%
+#Lineage	Family	Spoligotype	RD	Agreement
 
 #CHR	GENE	IDENTIFIER	PRODUCT	TYPE	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHAWAY
diff -r 02d81b994ef5 -r adc0645b945c test-data/rif_resistant_variants_report_with_lineage.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rif_resistant_variants_report_with_lineage.html	Wed Jul 07 09:22:44 2021 +0000
@@ -0,0 +1,113 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+        <title></title>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+    <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" rel="stylesheet"
+        integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
+    <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css">
+    <link rel="stylesheet" type="text/css"
+        href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.bootstrap4.min.css">
+    <link rel="stylesheet" type="text/css"
+        href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.dataTables.min.css">
+    </head>
+
+<body>
+    <div class="container">
+        <div class="row">
+            <h2 class="mt-5">
+                rif_resistant Report
+            </h2>
+        </div>
+                        <hr>
+        <div class="row justify-content-center align-items-center">
+    <table id="lineagereport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">
+        <thead class="thead-light">
+            <tr>
+                <th scope="col">Lineage</th>
+                <th scope="col">Family</th>
+                <th scape="col">Spoligotype</th>
+                <th scope="col">RD</th>
+                <th scope="col">Agreement</th>
+            </tr>
+        </thead>
+        <tbody>
+                        <tr>
+                <td>lineage2</td>
+                <td>East-Asian</td>
+                <td>Beijing</td>
+                <td>RD105</td>
+                <td>1.0</td>
+            </tr>
+                        <tr>
+                <td>lineage2.2</td>
+                <td>East-Asian (Beijing)</td>
+                <td>Beijing-RD207</td>
+                <td>RD105;RD207</td>
+                <td>1.0</td>
+            </tr>
+                        <tr>
+                <td>lineage2.2.2</td>
+                <td>East-Asian (Beijing)</td>
+                <td>Beijing-RD105/RD207</td>
+                <td>RD105;RD207</td>
+                <td>1.0</td>
+            </tr>
+                    </tbody>
+    </table>
+</div>
+<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>
+                <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
+            integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous">
+        </script>
+        <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js"
+            integrity="sha384-ZMP7rVo3mIykV+2+9J3UJ46jBk0WLaUAdn689aCwoqbBJiSnjAK/l8WvCWPIPm49" crossorigin="anonymous">
+        </script>
+        <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js"
+            integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy" crossorigin="anonymous">
+        </script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdn.datatables.net/buttons/1.5.2/js/dataTables.buttons.min.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.bootstrap4.min.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.flash.min.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.1.3/jszip.min.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.html5.min.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.print.min.js"></script>
+        <script type="text/javascript" charset="utf8"
+            src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.colVis.min.js"></script>
+        <script type="text/javascript" language="javascript" class="init">
+            $(function () {
+                var table = $('#vcfreport').DataTable({
+                    lengthChange: false,
+                    buttons: [{
+                        extend: 'csv',
+                        text: 'Download CSV',
+                        filename: 'rif_resistant'
+                    }]
+                });
+                table.buttons().container().appendTo('#vcfreport_wrapper .col-md-6:eq(0)');
+            });
+        </script>
+            </div>
+</body>
+
+</html>
\ No newline at end of file
diff -r 02d81b994ef5 -r adc0645b945c test-data/rif_resistant_variants_report_with_lineage.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rif_resistant_variants_report_with_lineage.txt	Wed Jul 07 09:22:44 2021 +0000
@@ -0,0 +1,7 @@
+#Rif_resistant Report
+#Lineage	Family	Spoligotype	RD	Agreement
+lineage2	East-Asian	Beijing	RD105	1.0
+lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207	1.0
+lineage2.2.2	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207	1.0
+
+#CHR	GENE	IDENTIFIER	PRODUCT	TYPE	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHAWAY