# HG changeset patch
# User iuc
# Date 1737839783 0
# Node ID 00e3b4ef7e0cd5ac135964456b22cf12415867df
# Parent  ec045ca00b50e9703e7bafa196b9b2346d2cc8e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 37e664b4211a39ac3dba2adb871c0b0ec80a4215

diff -r ec045ca00b50 -r 00e3b4ef7e0c jgi_summarize_bam_contig_depths.xml
--- a/jgi_summarize_bam_contig_depths.xml	Thu Nov 09 12:24:01 2023 +0000
+++ b/jgi_summarize_bam_contig_depths.xml	Sat Jan 25 21:16:23 2025 +0000
@@ -152,7 +152,15 @@
                 <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">
@@ -160,7 +168,14 @@
                 <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 @@
             <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"/>
@@ -199,7 +221,14 @@
             <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"/>
@@ -207,6 +236,7 @@
         </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 -r ec045ca00b50 -r 00e3b4ef7e0c macros.xml
--- a/macros.xml	Thu Nov 09 12:24:01 2023 +0000
+++ b/macros.xml	Sat Jan 25 21:16:23 2025 +0000
@@ -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 -r ec045ca00b50 -r 00e3b4ef7e0c test-data/jgi_output1.tabular
--- a/test-data/jgi_output1.tabular	Thu Nov 09 12:24:01 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-contigName	contigLen	totalAvgDepth	
-gi|251831106|ref|NC_012920.1|	16569	0.667885	0.667885	50.6321
diff -r ec045ca00b50 -r 00e3b4ef7e0c test-data/jgi_output2.tabular
--- a/test-data/jgi_output2.tabular	Thu Nov 09 12:24:01 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-contigName	contigLen	totalAvgDepth	
-gi|251831106|ref|NC_012920.1|	16569	1.33577	0.667885	50.6321	0.667885	50.6321
diff -r ec045ca00b50 -r 00e3b4ef7e0c test-data/jgi_output_depth1.tabular
--- a/test-data/jgi_output_depth1.tabular	Thu Nov 09 12:24:01 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-contigName	contigLen	totalAvgDepth	
-NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97	7000	0	0	0