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Merge pull request #6543 from emarinier/tbprofiler
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Updating tb-profiler to 6.4.0
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@bgruening
bgruening authored Nov 16, 2024
2 parents 9fe04d2 + 7113e37 commit fe5de3e
Showing 1 changed file with 8 additions and 7 deletions.
15 changes: 8 additions & 7 deletions tools/tb-profiler/tb_profiler_profile.xml
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<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1" profile="20.09" license="AGPL-3.0-or-later">
<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09" license="AGPL-3.0-or-later">
<description>Infer strain types and drug resistance markers from sequences</description>
<macros>
<token name="@TOOL_VERSION@">6.2.1</token>
<token name="@TOOL_VERSION@">6.4.0</token>
</macros>
<xrefs>
<xref type="bio.tools">tb-profiler</xref>
</xrefs>
<requirements>
<requirement type="package" version="1.2.6">delly</requirement>
<requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
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#if str($fastq_or_bam.input_select) != "bam"
&& mv bam/tbprofiler.bam '${output_bam}'
#end if
&& bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.vcf.gz
&& bcftools view -Ov -o '${output_vcf}' vcf/tbprofiler.targets.vcf.gz
#if $output_format == "pdf"
&& mv results/tbprofiler.results.pdf '${output_pdf}'
#else if $output_format == "txt"
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<has_line line="Drug-resistance: RR-TB" />
<has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
<has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
<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" />
</assert_contents>
</output>
</test>
Expand All @@ -204,7 +205,7 @@
<has_line line="Drug-resistance: RR-TB" />
<has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
<has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
<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" />
</assert_contents>
</output>
</test>
Expand All @@ -223,7 +224,7 @@
<output name="output_txt">
<assert_contents>
<has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
<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" />
</assert_contents>
</output>
<output name="results_json">
Expand All @@ -244,7 +245,7 @@
<has_line line="Octal: 000000000000771" />
<has_line line="Drug-resistance: RR-TB" />
<has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
<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" />
</assert_contents>
</output>
</test>
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