Mercurial > repos > iuc > tbvcfreport

annotate tbvcfreport.xml @ 4:9793bc5d741b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit a8fe4cf3a77ffb0334533cccb57b7af5f7f89e3b
author iuc
date Fri, 07 Jun 2024 14:29:45 +0000
parents 42818629ec4c
children
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02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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1 <?xml version="1.0" ?>
3
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2 <tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="AGPL-3.0-or-later">
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3 <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description>
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4 <macros>
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5 <token name="@TOOL_VERSION@">1.0.1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 #if $adv.database_uri
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13 export DATABASE_URI='${adv.database_uri}' &&
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14 #end if
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16 #if not '.vcf' in str($input_vcf.element_identifier)
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17 #set $input_vcf_filename = str($input_vcf.element_identifier).replace(' ', '') + '.vcf'
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18 #else
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19 #set $input_vcf_filename = str($input_vcf.element_identifier).replace(' ', '')
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20 #end if
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22 ln -s '${input_vcf}' '${input_vcf_filename}' &&
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24 #set vcf_name = os.path.splitext(os.path.basename($input_vcf_filename))[0]
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26 #if $tbprofiler_json
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27 #if not '.json' in str($tbprofiler_json.element_identifier)
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28 #set $tbprofiler_report = str($tbprofiler_json.element_identifier).replace(' ', '') + '.json'
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29 #else
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30 #set $tbprofiler_report = str($tbprofiler_json.element_identifier).replace(' ', '')
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31 #end if
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32 ln -s '${tbprofiler_json}' '${tbprofiler_report}' &&
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33 #end if
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35 tbvcfreport generate
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37 $filter_udi
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39 #if $tbprofiler_json
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40 --tbprofiler-report '${tbprofiler_report}'
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41 #end if
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43 '${input_vcf_filename}' &&
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45 #set variants_report = str(vcf_name) + '_variants_report'
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46 #set html_variants_report = variants_report + '.html'
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47 #set txt_variants_report = variants_report + '.txt'
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49 mv '${html_variants_report}' '$variants_report_html' &&
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50 mv '${txt_variants_report}' '$variants_report_txt'
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52 #if $tbprofiler_json
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53 #set drug_resistance_report = str(vcf_name) + '_drug_resistance_report'
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54 #set html_drug_resistance_report = drug_resistance_report + '.html'
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55 #set txt_drug_resistance_report = drug_resistance_report + '.txt'
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56
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57 && mv '${html_drug_resistance_report}' '$drug_resistance_report_html'
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58 && mv '${txt_drug_resistance_report}' '$drug_resistance_report_txt'
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59 #end if
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60 ]]>
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61 </command>
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62 <inputs>
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63 <param name="input_vcf" type="data" format="vcf" label="Input SnpEff annotated M.tuberculosis VCF(s)" />
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64 <param name="tbprofiler_json" type="data" format="json" optional="true" label="TBProfiler Drug Resistance Report (Optional)" help="--tbprofiler-report" />
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65 <param argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" />
0
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66 <section name="adv" title="Advanced options" expanded="false">
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67 <param name="database_uri" type="text" optional="true" value="neodb.sanbi.ac.za" label="Specify COMBAT-TB-NeoDB URI" help="For people with their own deployment of COMBAT-TB-NeoDB" />
0
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68 </section>
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69 </inputs>
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70 <outputs>
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71 <data name="variants_report_html" format="html" label="${tool.name} variants report (html) on ${on_string}" />
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72 <data name="variants_report_txt" format="txt" label="${tool.name} variants report (text) on ${on_string}" />
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73 <data name="drug_resistance_report_html" format="html" label="${tool.name} drug resistance report (html) on ${on_string}">
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74 <filter>tbprofiler_json</filter>
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75 </data>
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76 <data name="drug_resistance_report_txt" format="txt" label="${tool.name} drug resistance report (text) on ${on_string}">
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77 <filter>tbprofiler_json</filter>
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78 </data>
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79 </outputs>
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80 <tests>
2
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81 <test expect_num_outputs="2">
0
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82 <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" />
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83 <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report.html" ftype="html" />
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84 <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report.txt" ftype="txt" />
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85 </test>
2
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86 <test expect_num_outputs="4">
0
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87 <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" />
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88 <param name="tbprofiler_json" value="rif_resistant.results.json" ftype="json" />
1
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89 <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report_with_lineage.html" ftype="html" />
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90 <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report_with_lineage.txt" ftype="txt" />
0
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91 <output name="drug_resistance_report_html" file="rif_resistant_drug_resistance_report.html" lines_diff="2" ftype="html" />
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92 <output name="drug_resistance_report_txt" compare="diff" lines_diff="2" file="rif_resistant_drug_resistance_report.txt" ftype="txt" />
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93 </test>
2
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94 <test expect_num_outputs="2">
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95 <!-- test for bug fixed in 0.1.9 onwards: a gene with no protein product -->
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96 <param name="input_vcf" value="vcf_with_no_protein.vcf" ftype="vcf" />
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97 <output name="variants_report_html" compare="diff" lines_diff="2" file="vcf_with_no_protein_report.html" ftype="html" />
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98 <output name="variants_report_txt" compare="diff" lines_diff="2" file="vcf_with_no_protein_report.txt" ftype="txt" />
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99 </test>
0
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100 </tests>
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101 <help>
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102 <![CDATA[
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103 **tbvcfreport - @TOOL_VERSION@**
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104
3
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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105 **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB
0
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106 and links to Combat-TB-eXplorer (https://explorer.sanbi.ac.za/).
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107
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108 **tbvcfreport** will generate an HTML-based Drug Resistance report if provided with a TBProfiler json report.
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109
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110 Drug resistance predictions are for **Research Purposes Only** and are produced by TBProfiler (https://github.com/jodyphelan/TBProfiler)
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111
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112 **Inputs**
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113
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114 - SnpEff annotated M.tuberculosis VCF file(s) - vcf - **required**
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115
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116 - TBProfiler Drug Resistance JSON Report - json - **optional**
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117
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118 **Outputs**
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119
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120 - Variant Report in HTML and TXT format
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121
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122 - Drug Resistance Report in HTML and TXT format if provided with a TBProfiler json report
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123
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124
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125 **Advanced options**:
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126
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127 - database_uri - String - Use an on-premise COMBAT-TB-NeoDB (default 'neodb.sanbi.ac.za') - **optional**
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128
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129 **Further information**
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130
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131 For more on the **COMBAT-TB Project**, see https://combattb.org.
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132
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133 For more on **tbvcfreport**, see https://github.com/COMBAT-TB/tbvcfreport.
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134
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135 For more on **COMBAT-TB-NeoDB**, see https://github.com/COMBAT-TB/combat-tb-neodb.
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136 ]]>
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137 </help>
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138 <citations>
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139 <citation type="bibtex">
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140 @misc{githubtbvcfreport,
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141 author = {COMBAT-TB},
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142 year = {2019},
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143 title = {tbvcfreport},
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144 publisher = {GitHub},
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145 journal = {GitHub repository},
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146 url = {https://github.com/COMBAT-TB/tbvcfreport},
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147 }</citation>
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148 </citations>
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149 </tool>