Mercurial > repos > iuc > tbprofiler
comparison tb_profiler_profile.xml @ 9:e1a9d6fd258d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 9fa7ac6aaaf97db392a1bf93741a6d271b619ed3"
| author | iuc |
|---|---|
| date | Sat, 22 May 2021 17:10:13 +0000 |
| parents | 200c378d85f3 |
| children | 37213cf56392 |
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| 8:037a11682176 | 9:e1a9d6fd258d |
|---|---|
| 1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1"> | 1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1" profile="21.01"> |
| 2 <description>Infer strain types and drug resistance markers from sequences</description> | 2 <description>Infer strain types and drug resistance markers from sequences</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <token name="@TOOL_VERSION@">3.0.4</token> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 7 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement> | 7 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement> |
| 8 </requirements> | 8 </requirements> |
| 9 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
| 89 <when value="bam"> | 89 <when value="bam"> |
| 90 <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/> | 90 <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/> |
| 91 </when> | 91 </when> |
| 92 </conditional> | 92 </conditional> |
| 93 <param name="output_format" label="Output format" type="select"> | 93 <param name="output_format" label="Output format" type="select"> |
| 94 <option value="txt">Text</option> | 94 <option value="txt" selected="true">Text</option> |
| 95 <option value="pdf">PDF</option> | 95 <option value="pdf">PDF</option> |
| 96 </param> | 96 </param> |
| 97 <conditional name="advanced"> | 97 <conditional name="advanced"> |
| 98 <param label="Select advanced options" type="select" name="options"> | 98 <param label="Select advanced options" type="select" name="options"> |
| 99 <option value="yes">Yes</option> | 99 <option value="yes">Yes</option> |
| 126 <filter>output_format == 'txt'</filter> | 126 <filter>output_format == 'txt'</filter> |
| 127 </data> | 127 </data> |
| 128 | 128 |
| 129 </outputs> | 129 </outputs> |
| 130 <tests> | 130 <tests> |
| 131 <test> | 131 <test expect_num_outputs="4"> |
| 132 <param name="input_select" value="single_fastq"/> | 132 <param name="input_select" value="single_fastq"/> |
| 133 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" /> | 133 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" /> |
| 134 <param name="output_format" value="txt" /> | 134 <param name="output_format" value="txt" /> |
| 135 <param name="platform" value="illumina" /> | 135 <param name="platform" value="illumina" /> |
| 136 <param name="options" value="no" /> | 136 <param name="options" value="no" /> |
| 137 <output name="output_txt"> | 137 <output name="output_txt"> |
| 138 <assert_contents> | 138 <assert_contents> |
| 139 <has_line line="Drug-resistance: Drug-resistant" /> | 139 <has_line line="Drug-resistance: Pre-MDR" /> |
| 140 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207" /> | 140 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207" /> |
| 141 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> | 141 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> |
| 142 <has_line line="763031	Rv0667	rpoB	c.3225T>C	1.000" /> | 142 <has_line line="763031	Rv0667	rpoB	c.3225T>C	1.000" /> |
| 143 </assert_contents> | 143 </assert_contents> |
| 144 </output> | 144 </output> |
| 145 </test> | 145 </test> |
| 146 <test> | 146 <test expect_num_outputs="3"> |
| 147 <param name="input_select" value="bam"/> | 147 <param name="input_select" value="bam"/> |
| 148 <param name="bam_input" ftype="bam" value="rif_resistant.bam" /> | 148 <param name="bam_input" ftype="bam" value="rif_resistant.bam" /> |
| 149 <param name="output_format" value="txt" /> | 149 <param name="output_format" value="txt" /> |
| 150 <param name="platform" value="illumina" /> | 150 <param name="platform" value="illumina" /> |
| 151 <param name="options" value="no" /> | 151 <param name="options" value="no" /> |
| 152 <output name="output_txt"> | 152 <output name="output_txt"> |
| 153 <assert_contents> | 153 <assert_contents> |
| 154 <has_line line="Drug-resistance: Drug-resistant" /> | 154 <has_line line="Drug-resistance: Pre-MDR" /> |
| 155 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207" /> | 155 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207" /> |
| 156 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> | 156 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> |
| 157 <has_line line="763031	Rv0667	rpoB	c.3225T>C	1.000" /> | 157 <has_line line="763031	Rv0667	rpoB	c.3225T>C	1.000" /> |
| 158 </assert_contents> | 158 </assert_contents> |
| 159 </output> | 159 </output> |
| 160 </test> | 160 </test> |
| 161 <test> | 161 <test expect_num_outputs="4"> |
| 162 <param name="input_select" value="single_fastq"/> | 162 <param name="input_select" value="single_fastq"/> |
| 163 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" /> | 163 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" /> |
| 164 <param name="output_format" value="txt" /> | 164 <param name="output_format" value="txt" /> |
| 165 <param name="platform" value="illumina" /> | 165 <param name="platform" value="illumina" /> |
| 166 <param name="options" value="yes" /> | 166 <param name="options" value="yes" /> |
| 167 <param name="call_whole_genome" value="true" /> | 167 <param name="call_whole_genome" value="true" /> |
| 168 <param name="min_allele_freq" value="0.25" /> | 168 <param name="min_allele_freq" value="0.25" /> |
| 169 <param name="min_allele_freq_reporting" value="0.33" /> | 169 <param name="min_allele_freq_reporting" value="0.33" /> |
| 170 <output name="output_txt"> | 170 <output name="output_txt"> |
| 171 <assert_contents> | 171 <assert_contents> |
| 172 <has_line line="Drug-resistance: Drug-resistant" /> | 172 <has_line line="Drug-resistance: Pre-MDR" /> |
| 173 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207" /> | 173 <has_line line="lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207" /> |
| 174 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> | 174 <has_line line="Rifampicin	R	rpoB p.Asp435Val (1.00)" /> |
| 175 <has_line line="763031	Rv0667	rpoB	c.3225T>C	1.000" /> | 175 <has_line line="763031	Rv0667	rpoB	c.3225T>C	1.000" /> |
| 176 </assert_contents> | 176 </assert_contents> |
| 177 </output> | 177 </output> |
| 179 </tests> | 179 </tests> |
| 180 <help><![CDATA[ | 180 <help><![CDATA[ |
| 181 Summary | 181 Summary |
| 182 ======= | 182 ======= |
| 183 | 183 |
| 184 The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using GATK. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data). | 184 The pipeline aligns reads to the H37Rv reference using BWA, bowtie2 or minimap2 and then calls variants |
| 185 (using bcftools, GATK4 or freebayes). These variants are then compared to a drug-resistance database. | |
| 186 TB-Profiler also predicts the number of reads supporting drug resistance variants as an insight into | |
| 187 hetero-resistance (not applicable for MinION data). | |
| 185 | 188 |
| 186 Produces a JSON output file by default. | 189 Produces a JSON output file by default. |
| 187 | 190 |
| 188 ]]> </help> | 191 ]]> </help> |
| 189 <citations> | 192 <citations> |
| 190 <citation type="bibtex"> | 193 <citation type="doi">10.1186/s13073-019-0650-x</citation> |
| 191 @UNPUBLISHED{Phelan2016, | |
| 192 author = {Phelan, Jody}, | |
| 193 title = {TBProfiler}, | |
| 194 year = {2016}, | |
| 195 url = {https://github.com/jodyphelan/TBProfiler}, | |
| 196 } | |
| 197 </citation> | |
| 198 </citations> | 194 </citations> |
| 199 </tool> | 195 </tool> |