From fb94337b09338fbe4fa481854b57e8d1978cb760 Mon Sep 17 00:00:00 2001
From: Eric <emarinier@gmail.com>
Date: Fri, 8 Nov 2024 13:46:52 -0600
Subject: [PATCH 1/6] Updating to 6.4.0

---
 tools/tb-profiler/tb_profiler_profile.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/tb-profiler/tb_profiler_profile.xml b/tools/tb-profiler/tb_profiler_profile.xml
index 3656dcaa953..23daf1c16d8 100644
--- a/tools/tb-profiler/tb_profiler_profile.xml
+++ b/tools/tb-profiler/tb_profiler_profile.xml
@@ -1,7 +1,7 @@
-<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>
@@ -189,7 +189,7 @@
                     <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 +204,7 @@
                     <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 +223,7 @@
             <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 +244,7 @@
                     <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>

From 4913122a90ff1c6bbffca21b81e29e64e6755c0d Mon Sep 17 00:00:00 2001
From: Eric <emarinier@gmail.com>
Date: Fri, 8 Nov 2024 15:50:02 -0600
Subject: [PATCH 2/6] Testing adding prefix to file output.

---
 tools/tb-profiler/tb_profiler_profile.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/tb-profiler/tb_profiler_profile.xml b/tools/tb-profiler/tb_profiler_profile.xml
index 23daf1c16d8..a31ef70be64 100644
--- a/tools/tb-profiler/tb_profiler_profile.xml
+++ b/tools/tb-profiler/tb_profiler_profile.xml
@@ -30,6 +30,7 @@
         #end if
 
         tb-profiler profile
+            --prefix tbprofiler
             --platform '${platform.value}'
             ${spoligotype}
         #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
@@ -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"

From 8853f3a7c706c565ede021836f4df961c8ff6664 Mon Sep 17 00:00:00 2001
From: Eric <emarinier@gmail.com>
Date: Tue, 12 Nov 2024 11:02:09 -0600
Subject: [PATCH 3/6] Debugging

---
 tools/tb-profiler/tb_profiler_profile.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/tb-profiler/tb_profiler_profile.xml b/tools/tb-profiler/tb_profiler_profile.xml
index a31ef70be64..e1f96012147 100644
--- a/tools/tb-profiler/tb_profiler_profile.xml
+++ b/tools/tb-profiler/tb_profiler_profile.xml
@@ -68,6 +68,7 @@
         #if str($fastq_or_bam.input_select) != "bam"
             && mv bam/tbprofiler.bam '${output_bam}'
         #end if
+        && ls -la; ls -la vcf
         && bcftools view -Ov -o '${output_vcf}' vcf/tbprofiler.targets.vcf.gz
         #if $output_format == "pdf"
             && mv results/tbprofiler.results.pdf '${output_pdf}'

From 89cee993df9e6b8ec39dc6276fd817c3340f06c3 Mon Sep 17 00:00:00 2001
From: Eric <emarinier@gmail.com>
Date: Tue, 12 Nov 2024 12:03:35 -0600
Subject: [PATCH 4/6] Testing fixing delly version.

---
 tools/tb-profiler/tb_profiler_profile.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/tb-profiler/tb_profiler_profile.xml b/tools/tb-profiler/tb_profiler_profile.xml
index e1f96012147..ec9e621cdb5 100644
--- a/tools/tb-profiler/tb_profiler_profile.xml
+++ b/tools/tb-profiler/tb_profiler_profile.xml
@@ -7,6 +7,7 @@
         <xref type="bio.tools">tb-profiler</xref>
     </xrefs>
     <requirements>
+        <requirement type="package" version="0.8.7">delly</requirement>
         <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[

From f7d05179f307b8cb4da05b993a80de6cefa0f2ec Mon Sep 17 00:00:00 2001
From: Eric <emarinier@gmail.com>
Date: Tue, 12 Nov 2024 14:15:15 -0600
Subject: [PATCH 5/6] delly 1.2.6

---
 tools/tb-profiler/tb_profiler_profile.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/tb-profiler/tb_profiler_profile.xml b/tools/tb-profiler/tb_profiler_profile.xml
index ec9e621cdb5..81e60e029c0 100644
--- a/tools/tb-profiler/tb_profiler_profile.xml
+++ b/tools/tb-profiler/tb_profiler_profile.xml
@@ -7,7 +7,7 @@
         <xref type="bio.tools">tb-profiler</xref>
     </xrefs>
     <requirements>
-        <requirement type="package" version="0.8.7">delly</requirement>
+        <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[

From 7113e3791a0d6bbf2dbafe268a85b021a01153b8 Mon Sep 17 00:00:00 2001
From: Eric <emarinier@gmail.com>
Date: Tue, 12 Nov 2024 14:33:16 -0600
Subject: [PATCH 6/6] Removing debug code.

---
 tools/tb-profiler/tb_profiler_profile.xml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tools/tb-profiler/tb_profiler_profile.xml b/tools/tb-profiler/tb_profiler_profile.xml
index 81e60e029c0..bc69616d6f8 100644
--- a/tools/tb-profiler/tb_profiler_profile.xml
+++ b/tools/tb-profiler/tb_profiler_profile.xml
@@ -31,7 +31,6 @@
         #end if
 
         tb-profiler profile
-            --prefix tbprofiler
             --platform '${platform.value}'
             ${spoligotype}
         #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
@@ -69,7 +68,6 @@
         #if str($fastq_or_bam.input_select) != "bam"
             && mv bam/tbprofiler.bam '${output_bam}'
         #end if
-        && ls -la; ls -la vcf
         && bcftools view -Ov -o '${output_vcf}' vcf/tbprofiler.targets.vcf.gz
         #if $output_format == "pdf"
             && mv results/tbprofiler.results.pdf '${output_pdf}'