# HG changeset patch
# User bgruening
# Date 1634824061 0
# Node ID 5d7c5ae1b69b8d6e54fe6970d95304cab26aa8dc
# Parent  96cacb31d5719b93b930e391c818e42fbcdf02c1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"

diff -r 96cacb31d571 -r 5d7c5ae1b69b bionano_scaffold.xml
--- a/bionano_scaffold.xml	Sat May 29 15:58:03 2021 +0000
+++ b/bionano_scaffold.xml	Thu Oct 21 13:47:41 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
+<tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>automates the scaffolding process</description>
     <macros>
         <import>macros.xml</import>
@@ -58,7 +58,7 @@
         #if $trim_cut_sites
             && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log'
             && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log'
-        #end if        
+        #end if 
     ]]>    </command>
     <configfiles>
         <configfile name="vgp_mode"><![CDATA[
@@ -437,9 +437,10 @@
         <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">
             <filter>zip_file</filter>
         </data>
+        <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/>
     </outputs>
     <tests>
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="6">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="3"/>
@@ -463,6 +464,7 @@
                 </assert_contents>
             </output>
             <output name="report" file="test_01_report.txt" ftype="txt"/>
+            <output name="ngs_contigs_scaffold_agp" file="test_01.agp" ftype="agp"/>
             <output name="conflicts" ftype="txt">
                 <assert_contents>
                     <has_text text="alignmentOrientation" />
@@ -490,7 +492,7 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="5">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="2"/>
@@ -513,6 +515,13 @@
                 </assert_contents>
             </output>
             <output name="report" file="test_02_report.txt" ftype="txt"/>
+            <output name="ngs_contigs_scaffold_agp" ftype="agp">
+                <assert_contents>
+                    <has_size value="311" delta="20" />
+                    <has_text text="##agp-version"/>
+                    <has_n_lines n="9"/>
+                </assert_contents>
+            </output>
             <output name="conflicts" ftype="txt">
                 <assert_contents>
                     <has_text text="alignmentOrientation" />
@@ -534,7 +543,7 @@
                 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/-->
             </assert_stdout>
         </test>
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="6">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="2"/>
@@ -558,6 +567,13 @@
                 </assert_contents>
             </output>
             <output name="report" file="test_03_report.txt" ftype="txt"/>
+            <output name="ngs_contigs_scaffold_agp" ftype="agp">
+                <assert_contents>
+                    <has_size value="311" delta="20" />
+                    <has_text text="##agp-version"/>
+                    <has_n_lines n="9"/>
+                </assert_contents>
+            </output>
             <output name="conflicts" ftype="txt">
                 <assert_contents>
                     <has_text text="alignmentOrientation" />
@@ -585,7 +601,7 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="6">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="2"/>
@@ -609,6 +625,13 @@
                 </assert_contents>
             </output>
             <output name="report" file="test_04_report.txt" ftype="txt"/>
+            <output name="ngs_contigs_scaffold_agp" ftype="agp">
+                <assert_contents>
+                    <has_size value="311" delta="20" />
+                    <has_text text="##agp-version"/>
+                    <has_n_lines n="9"/>
+                </assert_contents>
+            </output>
             <output name="conflicts" ftype="txt">
                 <assert_contents>
                     <has_text text="alignmentOrientation" />
@@ -635,7 +658,7 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="5">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="3"/>
@@ -663,6 +686,13 @@
                 </assert_contents>
             </output>            
             <output name="report" file="test_05_report.txt" ftype="txt"/>
+            <output name="ngs_contigs_scaffold_agp" ftype="agp">
+                <assert_contents>
+                    <has_size value="311" delta="20" />
+                    <has_text text="##agp-version"/>
+                    <has_n_lines n="9"/>
+                </assert_contents>
+            </output>
             <assert_stdout>
                 <has_text text='attr="maxmem" val0="8"'/>
             </assert_stdout>
diff -r 96cacb31d571 -r 5d7c5ae1b69b macros.xml
--- a/macros.xml	Sat May 29 15:58:03 2021 +0000
+++ b/macros.xml	Thu Oct 21 13:47:41 2021 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.6.1</token>
-    <token name="@GALAXY_TOOL_VERSION@">galaxy2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@BIONANO_SUPPORT_TEXT@">
 Bionano Genomics has agreed to provide the licensed Bionano Solve
 software to enable the VGP to package the software in a container.
diff -r 96cacb31d571 -r 5d7c5ae1b69b test-data/test_02.agp
--- a/test-data/test_02.agp	Sat May 29 15:58:03 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-##agp-version	2.0
-# Organism:  
-# Platform:     
-# Model:        
-# Enzyme(s):    
-# BioSample:    
-# BioProject:   
-# Obj_Name	Obj_Start	Obj_End	PartNum	Compnt_Type	CompntId_GapLength	CompntStart_GapType	CompntEnd_Linkage	Orientation_LinkageEvidence
-Super-Scaffold_1	1	4753350	1	W	Super_scaffold_3	1	4753350	+
diff -r 96cacb31d571 -r 5d7c5ae1b69b test-data/test_03.agp
--- a/test-data/test_03.agp	Sat May 29 15:58:03 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-##agp-version	2.0
-# Organism:  
-# Platform:     
-# Model:        
-# Enzyme(s):    
-# BioSample:    
-# BioProject:   
-# Obj_Name	Obj_Start	Obj_End	PartNum	Compnt_Type	CompntId_GapLength	CompntStart_GapType	CompntEnd_Linkage	Orientation_LinkageEvidence
-Super-Scaffold_1	1	4753350	1	W	Super_scaffold_3	1	4753350	+
diff -r 96cacb31d571 -r 5d7c5ae1b69b test-data/test_04.agp
--- a/test-data/test_04.agp	Sat May 29 15:58:03 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-##agp-version	2.0
-# Organism:  
-# Platform:     
-# Model:        
-# Enzyme(s):    
-# BioSample:    
-# BioProject:   
-# Obj_Name	Obj_Start	Obj_End	PartNum	Compnt_Type	CompntId_GapLength	CompntStart_GapType	CompntEnd_Linkage	Orientation_LinkageEvidence
-Super-Scaffold_1	1	4753350	1	W	Super_scaffold_3	1	4753350	+