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comparison tb_profiler_profile.xml @ 20:8cb134b8c1a5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit fe5de3e1e0dc056c102ed13c9553ef2e0d6fcab6
author iuc
date Sat, 16 Nov 2024 20:26:57 +0000
parents 51dd22484644
children
comparison
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19:51dd22484644 20:8cb134b8c1a5
1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1" profile="20.09" license="AGPL-3.0-or-later"> 1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09" license="AGPL-3.0-or-later">
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@">6.2.1</token> 4 <token name="@TOOL_VERSION@">6.4.0</token>
5 </macros> 5 </macros>
6 <xrefs> 6 <xrefs>
7 <xref type="bio.tools">tb-profiler</xref> 7 <xref type="bio.tools">tb-profiler</xref>
8 </xrefs> 8 </xrefs>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="1.2.6">delly</requirement>
10 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
11 </requirements> 12 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
13 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq") 14 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
14 #if str($fastq_or_bam.input_select.value) == "paired_fastq" 15 #if str($fastq_or_bam.input_select.value) == "paired_fastq"
65 #end if 66 #end if
66 && mv results/tbprofiler.results.json $results_json 67 && mv results/tbprofiler.results.json $results_json
67 #if str($fastq_or_bam.input_select) != "bam" 68 #if str($fastq_or_bam.input_select) != "bam"
68 && mv bam/tbprofiler.bam '${output_bam}' 69 && mv bam/tbprofiler.bam '${output_bam}'
69 #end if 70 #end if
70 && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.vcf.gz 71 && bcftools view -Ov -o '${output_vcf}' vcf/tbprofiler.targets.vcf.gz
71 #if $output_format == "pdf" 72 #if $output_format == "pdf"
72 && mv results/tbprofiler.results.pdf '${output_pdf}' 73 && mv results/tbprofiler.results.pdf '${output_pdf}'
73 #else if $output_format == "txt" 74 #else if $output_format == "txt"
74 && mv results/tbprofiler.results.txt '${output_txt}' 75 && mv results/tbprofiler.results.txt '${output_txt}'
75 #end if 76 #end if
187 <output name="output_txt"> 188 <output name="output_txt">
188 <assert_contents> 189 <assert_contents>
189 <has_line line="Drug-resistance: RR-TB" /> 190 <has_line line="Drug-resistance: RR-TB" />
190 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" /> 191 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
191 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 192 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
192 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" /> 193 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
193 </assert_contents> 194 </assert_contents>
194 </output> 195 </output>
195 </test> 196 </test>
196 <test expect_num_outputs="3"> 197 <test expect_num_outputs="3">
197 <param name="input_select" value="bam"/> 198 <param name="input_select" value="bam"/>
202 <output name="output_txt"> 203 <output name="output_txt">
203 <assert_contents> 204 <assert_contents>
204 <has_line line="Drug-resistance: RR-TB" /> 205 <has_line line="Drug-resistance: RR-TB" />
205 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" /> 206 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
206 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 207 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
207 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" /> 208 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
208 </assert_contents> 209 </assert_contents>
209 </output> 210 </output>
210 </test> 211 </test>
211 <test expect_num_outputs="4"> 212 <test expect_num_outputs="4">
212 <param name="input_select" value="single_fastq"/> 213 <param name="input_select" value="single_fastq"/>
221 </section> 222 </section>
222 </conditional> 223 </conditional>
223 <output name="output_txt"> 224 <output name="output_txt">
224 <assert_contents> 225 <assert_contents>
225 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" /> 226 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
226 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" /> 227 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
227 </assert_contents> 228 </assert_contents>
228 </output> 229 </output>
229 <output name="results_json"> 230 <output name="results_json">
230 <assert_contents> 231 <assert_contents>
231 <has_text text='"filter": "soft_fail",' /> 232 <has_text text='"filter": "soft_fail",' />
242 <output name="output_txt"> 243 <output name="output_txt">
243 <assert_contents> 244 <assert_contents>
244 <has_line line="Octal: 000000000000771" /> 245 <has_line line="Octal: 000000000000771" />
245 <has_line line="Drug-resistance: RR-TB" /> 246 <has_line line="Drug-resistance: RR-TB" />
246 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" /> 247 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
247 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" /> 248 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;35&#009;1.000&#009;rifampicin&#009;Assoc w R" />
248 </assert_contents> 249 </assert_contents>
249 </output> 250 </output>
250 </test> 251 </test>
251 </tests> 252 </tests>
252 <help><![CDATA[ 253 <help><![CDATA[