Merge pull request #6686 from SantaMcCloud/update_metabat2

Update MetaBAT2 from 2.15 to 2.17
galaxyproject · Jan 25, 2025 · 37e664b · 37e664b
2 parents f43fe42 + 083bde6
commit 37e664b
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Showing 5 changed files with 36 additions and 12 deletions.
diff --git a/tools/metabat2/jgi_summarize_bam_contig_depths.xml b/tools/metabat2/jgi_summarize_bam_contig_depths.xml
@@ -152,15 +152,30 @@ jgi_summarize_bam_contig_depths
                 <param name="type" value="individual"/>
                 <param name="bam_indiv_input" value="input1.bam" ftype="bam"/>
             </conditional>
-            <output name="outputDepth" file="jgi_output1.tabular" ftype="tabular" compare="contains"/>
+            <output name="outputDepth" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="5"/> 
+                    <has_text text="50.6321"/>
+                    <has_text text="16569"/>
+                    <has_text text="gi|251831106|ref|NC_012920.1|"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Multiple inputs, default settings -->
         <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="type" value="co"/>
                 <param name="bam_co_inputs" value="input1.bam,input1.bam" ftype="bam"/>
             </conditional>
-            <output name="outputDepth" file="jgi_output2.tabular" ftype="tabular" compare="contains"/>
+            <output name="outputDepth" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="7"/> 
+                    <has_text text="16569"/>
+                    <has_text text="gi|251831106|ref|NC_012920.1|"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Single input, output paired contigs, reference from history -->
         <test expect_num_outputs="5">
@@ -178,7 +193,14 @@ jgi_summarize_bam_contig_depths
             <section name="advanced">
                 <param name="output_paired_contigs" value="true"/>
             </section>
-            <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>
+            <output name="outputDepth" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="5"/> 
+                    <has_text text="7000"/>
+                    <has_text text="NC_002945.4"/>
+                </assert_contents>
+            </output>
             <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>
             <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>
             <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/>
@@ -199,14 +221,22 @@ jgi_summarize_bam_contig_depths
             <section name="advanced">
                 <param name="output_paired_contigs" value="true"/>
             </section>
-            <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>
+            <output name="outputDepth" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="5"/> 
+                    <has_text text="7000"/>
+                    <has_text text="NC_002945.4"/>
+                </assert_contents>
+            </output>
             <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>
             <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>
             <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/>
             <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/>
         </test>
     </tests>
     <help><![CDATA[
+        
 **What it does**
 
 Calculates coverage depth for each sequence in one or more selected BAM files, producing a tabular file (for each input)

diff --git a/tools/metabat2/macros.xml b/tools/metabat2/macros.xml
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.15</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@TOOL_VERSION@">2.17</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
         <xrefs>

diff --git a/tools/metabat2/test-data/jgi_output1.tabular b/tools/metabat2/test-data/jgi_output1.tabular
diff --git a/tools/metabat2/test-data/jgi_output2.tabular b/tools/metabat2/test-data/jgi_output2.tabular
diff --git a/tools/metabat2/test-data/jgi_output_depth1.tabular b/tools/metabat2/test-data/jgi_output_depth1.tabular