# HG changeset patch
# User bgruening
# Date 1674055333 0
# Node ID 22286dab5aa1f9ee88beeace458c75ca36af7e12
# Parent  faee8629b460c14327e0dd7e8413125eea64ba6e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e

diff -r faee8629b460 -r 22286dab5aa1 bionano_scaffold.xml
--- a/bionano_scaffold.xml	Tue Dec 13 09:26:04 2022 +0000
+++ b/bionano_scaffold.xml	Wed Jan 18 15:22:13 2023 +0000
@@ -59,7 +59,9 @@
             && export PATH=/opt/conda/bin/:\$PATH
             && 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' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log'
-        #end if 
+        #end if
+        && echo >> hybrid_scaffolds/*cut.txt
+        && mv hybrid_scaffolds/*cut.txt hybrid_scaffolds/keys.txt
     ]]>    </command>
     <configfiles>
         <configfile name="vgp_mode"><![CDATA[
@@ -388,7 +390,7 @@
             <option value="2">Cut contig at conflict</option>
             <option value="3">Exclude conflicting contig</option>
         </param>
-        <param name="all_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Provide all files" help="Generate a collection with the files contained in the hybrid_scaffolds folder" />
+        <param name="all_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Provide BisCot required files" help="Generate a collection with the files contained in the hybrid_scaffolds folder" />
         <param name="zip_file" argument="-z" type="boolean" truevalue="-z results.zip" falsevalue="" checked="false" label="Generate an output package in ZIP format" help="The hybrid scaffold output package (.zip) can be imported into Access for visualization" />
         <param name="trim_cut_sites" type="boolean" checked="true" label="Remove BioNano cut sites" help="This option removes the spurious BioNano cut sites that are inserted into gaps in some assemblies, replacing them with Ns." />
         <!-- 
@@ -440,10 +442,19 @@
             <filter>zip_file</filter>
         </data>
         <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/>
-        <collection name="allfiles" type="list" label="${tool.name} on ${on_string}: hybrid scaffolds files">
-            <discover_datasets pattern="__name_and_ext__" directory="hybrid_scaffolds" />
+        
+        <data name="query_file" format="cmap" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap" label="${tool.name} on ${on_string}: query CMAP">
+            <filter>all_files</filter>
+        </data>
+        <data name="reference_file" format="cmap" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_r.cmap" label="${tool.name} on ${on_string}: reference CMAP">
             <filter>all_files</filter>
-        </collection>
+        </data>
+        <data name="xmap_file" format="xml" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap" label="${tool.name} on ${on_string}: XMAP configuration">
+            <filter>all_files</filter>
+        </data>
+        <data name="key_file" format="tabular" from_work_dir="hybrid_scaffolds/keys.txt" label="${tool.name} on ${on_string}: Bionano key file">
+            <filter>all_files</filter>
+        </data>
     </outputs>
     <tests>
         <test expect_num_outputs="6">
@@ -648,7 +659,7 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
-        <test expect_num_outputs="6">
+        <test expect_num_outputs="9">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="3"/>
@@ -679,14 +690,24 @@
                     <has_n_lines n="9"/>
                 </assert_contents>
             </output>
-            <output_collection name="allfiles" type="list" count="21">
-                <element name="BSPQI_bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_NGScontigs_q">
-                    <assert_contents>
-                        <has_text text="Number of Consensus Maps"/>
-                        <has_n_lines n="534" delta="50"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
+            <output name="query_file" ftype="cmap">
+                <assert_contents>
+                    <has_text text="3879935.1"/>
+                    <has_text text="Coverage refer to the interval between current site and next site"/>
+                </assert_contents>
+            </output>            
+            <output name="reference_file" ftype="cmap">
+                <assert_contents>
+                    <has_text text="4753350.0"/>
+                    <has_text text=" StdDev refers to the interval between the current site and the next site"/>
+                </assert_contents>
+            </output>            
+            <output name="xmap_file" ftype="xml">
+                <assert_contents>
+                    <has_text text="XMAP File Version"/>
+                    <has_text text="(7,7)(8,8)(9,9)(10,10)(11,11)(12,12)(13,13)"/>
+                </assert_contents>
+            </output>
             <assert_stdout>
                 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
                 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
diff -r faee8629b460 -r 22286dab5aa1 macros.xml
--- a/macros.xml	Tue Dec 13 09:26:04 2022 +0000
+++ b/macros.xml	Wed Jan 18 15:22:13 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.7.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</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.