Merge pull request #6543 from emarinier/tbprofiler

Updating tb-profiler to 6.4.0

Author: bgruening

tools/tb-profiler/tb_profiler_profile.xml

@@ -1,12 +1,13 @@
-<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[
@@ -67,7 +68,7 @@
         #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"
@@ -189,7 +190,7 @@
                     <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>
@@ -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>
@@ -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">
@@ -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>