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comparison tb_profiler_profile.xml @ 15:45083d070fb8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 9dd4c8aca212218a9e8f8a49013c255696191b0f
author iuc
date Sat, 31 Dec 2022 15:36:09 +0000
parents ac8250086ac3
children 2c68b0c38785
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14:ac8250086ac3 15:45083d070fb8
1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09"> 1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09">
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 <token name="@TOOL_VERSION@">4.1.1</token> 4 <token name="@TOOL_VERSION@">4.4.0</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[
65 ]]> </command> 65 ]]> </command>
66 <inputs> 66 <inputs>
67 <param name="platform" type="select" label="Platform"> 67 <param name="platform" type="select" label="Platform">
68 <option value="illumina" selected="true">Illumina</option> 68 <option value="illumina" selected="true">Illumina</option>
69 <option value="nanopore">Nanopore</option> 69 <option value="nanopore">Nanopore</option>
70 <option value="pacbio">PacBio</option>
70 </param> 71 </param>
71 <conditional name="fastq_or_bam"> 72 <conditional name="fastq_or_bam">
72 <param name="input_select" type="select" label="Input File Type"> 73 <param name="input_select" type="select" label="Input File Type">
73 <option value="paired_fastq">Paired Fastq</option> 74 <option value="paired_fastq">Paired Fastq</option>
74 <option value="paired_collection_fastq">Paired Collection Fastq</option> 75 <option value="paired_collection_fastq">Paired Collection Fastq</option>
142 <param name="platform" value="illumina" /> 143 <param name="platform" value="illumina" />
143 <param name="options" value="no" /> 144 <param name="options" value="no" />
144 <output name="output_txt"> 145 <output name="output_txt">
145 <assert_contents> 146 <assert_contents>
146 <has_line line="Drug-resistance: RR-TB" /> 147 <has_line line="Drug-resistance: RR-TB" />
147 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" /> 148 <has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
148 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 149 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
149 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" /> 150 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
150 </assert_contents> 151 </assert_contents>
151 </output> 152 </output>
152 </test> 153 </test>
153 <test expect_num_outputs="3"> 154 <test expect_num_outputs="3">
154 <param name="input_select" value="bam"/> 155 <param name="input_select" value="bam"/>
157 <param name="platform" value="illumina" /> 158 <param name="platform" value="illumina" />
158 <param name="options" value="no" /> 159 <param name="options" value="no" />
159 <output name="output_txt"> 160 <output name="output_txt">
160 <assert_contents> 161 <assert_contents>
161 <has_line line="Drug-resistance: RR-TB" /> 162 <has_line line="Drug-resistance: RR-TB" />
162 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" /> 163 <has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
163 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 164 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
164 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" /> 165 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
165 </assert_contents> 166 </assert_contents>
166 </output> 167 </output>
167 </test> 168 </test>
168 <test expect_num_outputs="4"> 169 <test expect_num_outputs="4">
169 <param name="input_select" value="single_fastq"/> 170 <param name="input_select" value="single_fastq"/>
170 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" /> 171 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
171 <param name="output_format" value="txt" /> 172 <param name="output_format" value="txt" />
172 <param name="platform" value="illumina" /> 173 <param name="platform" value="illumina" />
173 <param name="options" value="yes" /> 174 <param name="options" value="yes" />
174 <param name="call_whole_genome" value="true" />
175 <param name="min_allele_freq" value="0.25" /> 175 <param name="min_allele_freq" value="0.25" />
176 <param name="min_allele_freq_reporting" value="0.33" /> 176 <param name="min_allele_freq_reporting" value="0.33" />
177 <output name="output_txt"> 177 <output name="output_txt">
178 <assert_contents> 178 <assert_contents>
179 <has_line line="Drug-resistance: RR-TB" /> 179 <has_line line="Drug-resistance: RR-TB" />
180 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" /> 180 <has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
181 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 181 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
182 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" /> 182 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
183 </assert_contents> 183 </assert_contents>
184 </output> 184 </output>
185 </test> 185 </test>
186 </tests> 186 </tests>
187 <help><![CDATA[ 187 <help><![CDATA[