Merge pull request #5945 from mvdbeek/fix_containerized_merqury

Fix containerized merqury
galaxyproject · Apr 13, 2024 · 9aec17d · 9aec17d
2 parents 8722918 + e5fa216
commit 9aec17d
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Showing 6 changed files with 14 additions and 14 deletions.
diff --git a/tools/merqury/macros.xml b/tools/merqury/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">merqury</xref>
@@ -11,7 +11,7 @@
             <requirement type="package" version="@TOOL_VERSION@">merqury</requirement>
             <requirement type="package" version="1.34">tar</requirement>
             <requirement type="package" version="4.6.0">findutils</requirement>
-            <requirement type="package" version="8.32">coreutils</requirement>
+            <requirement type="package" version="9.5">coreutils</requirement>
         </requirements>
     </xml>
     <xml name="citations">

diff --git a/tools/merqury/merqury.xml b/tools/merqury/merqury.xml
@@ -236,32 +236,32 @@
             <output_collection name="png_files" type="list" count="6">
                 <element name="output_02.assembly.spectra-cn.fl">
                     <assert_contents>
-                        <has_size value="71874" delta="100"/>
+                        <has_size value="74570" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.assembly.spectra-cn.ln">
                     <assert_contents>
-                        <has_size value="71888" delta="100"/>
+                        <has_size value="74476" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.assembly.spectra-cn.st">
                     <assert_contents>
-                        <has_size value="71123" delta="100"/>
+                        <has_size value="74205" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.spectra-asm.fl">
                     <assert_contents>
-                        <has_size value="47245" delta="100"/>
+                        <has_size value="48524" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.spectra-asm.ln">
                     <assert_contents>
-                        <has_size value="46896" delta="100"/>
+                        <has_size value="48028" delta="100"/>
                     </assert_contents>
                 </element>
                 <element name="output_02.spectra-asm.st">
                     <assert_contents>
-                        <has_size value="45945" delta="100"/>
+                        <has_size value="47447" delta="100"/>
                     </assert_contents>
                 </element>
             </output_collection>

diff --git a/tools/merqury/merqury_plot_CN.xml b/tools/merqury/merqury_plot_CN.xml
@@ -6,9 +6,9 @@
     <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <version_command>merqury --version</version_command>
-
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p output_files/ &&
+        export MERQURY="\$(dirname \$(which merqury.sh))/../share/merqury" &&
         \$MERQURY/plot/plot_spectra_cn.R 
         -f '$input1' 
         -o output_files/merqury_plot

diff --git a/tools/merqury/test-data/output_02_qv.tabular b/tools/merqury/test-data/output_02_qv.tabular
@@ -1 +1 @@
-assembly	0	1037953		
+assembly	0	1037953	+inf	0
diff --git a/tools/merqury/test-data/output_03_qv.tabular b/tools/merqury/test-data/output_03_qv.tabular
@@ -1,3 +1,3 @@
-assembly_01	0	1037953		
-assembly_02	0	1037953		
-Both	0	2075906		
+assembly_01	0	1037953	+inf	0
+assembly_02	0	1037953	+inf	0
+Both	0	2075906	+inf	0
diff --git a/tools/merqury/test-data/output_06_qv.tabular b/tools/merqury/test-data/output_06_qv.tabular
@@ -1,2 +1,2 @@
 assembly	unique k-mers	common k-mers	QV	error rate
-assembly	0	1037953		
+assembly	0	1037953	+inf	0