Mercurial > repos > iuc > tbvcfreport
changeset 1:adc0645b945c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
| author | iuc |
|---|---|
| date | Wed, 07 Jul 2021 09:22:44 +0000 |
| parents | 02d81b994ef5 |
| children | 4934c0ac6197 |
| files | tbvcfreport.xml test-data/rif_resistant_drug_resistance_report.html test-data/rif_resistant_drug_resistance_report.txt test-data/rif_resistant_variants_report.html test-data/rif_resistant_variants_report.txt test-data/rif_resistant_variants_report_with_lineage.html test-data/rif_resistant_variants_report_with_lineage.txt |
| diffstat | 7 files changed, 128 insertions(+), 53 deletions(-) [+] |
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--- 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>
--- 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">
--- 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
--- 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"
--- 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
--- /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
--- /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