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comparison tb_profiler_profile.xml @ 9:e1a9d6fd258d draft

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"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&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" /> 140 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
141 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 141 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
142 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" /> 142 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;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&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" /> 155 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
156 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 156 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
157 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" /> 157 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;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&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" /> 173 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
174 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 174 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
175 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" /> 175 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;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>