# HG changeset patch
# User bgruening
# Date 1670923564 0
# Node ID faee8629b460c14327e0dd7e8413125eea64ba6e
# Parent  5258e18bbe2360cf19c866d231e26c6c9ba04fa1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158

diff -r 5258e18bbe23 -r faee8629b460 bionano_scaffold.xml
--- a/bionano_scaffold.xml	Sat Feb 05 18:15:29 2022 +0000
+++ b/bionano_scaffold.xml	Tue Dec 13 09:26:04 2022 +0000
@@ -374,7 +374,7 @@
                 </param>
             </when>
             <when value="file">
-                <param name="configuration_file" type="data" format="xml" label="Configuration file" help="Depending on the complexity of the genome of interest, the values of certain parameters could be adjusted accordingly."/>
+                <param name="configuration_file" type="data" format="xml,txt" label="Configuration file" help="Depending on the complexity of the genome of interest, the values of certain parameters could be adjusted accordingly."/>
             </when>
         </conditional>
         <param name="conflict_resolution" argument="-M" type="data" format="txt" optional="True" label="Conflict resolution file" help="Input a conflict resolution file indicating which NGS and BioNano conflicting contigs to be cut [optional]"/>
@@ -388,6 +388,7 @@
             <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="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." />
         <!-- 
@@ -439,6 +440,10 @@
             <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" />
+            <filter>all_files</filter>
+        </collection>
     </outputs>
     <tests>
         <test expect_num_outputs="6">
@@ -459,11 +464,6 @@
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_not_scaffolded" ftype="fasta">
-                <assert_contents>
-                    <has_size value="0"/>
-                </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">
@@ -478,17 +478,9 @@
             </output>
             <assert_stdout>
                 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
-            </assert_stdout>
-             <assert_stdout>
                 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
@@ -509,11 +501,6 @@
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_not_scaffolded" ftype="fasta">
-                <assert_contents>
-                    <has_size value="0"  />
-                </assert_contents>
-            </output>
             <output name="report" file="test_02_report.txt" ftype="txt"/>
             <output name="ngs_contigs_scaffold_agp" ftype="agp">
                 <assert_contents>
@@ -526,19 +513,12 @@
                 <assert_contents>
                     <has_text text="alignmentOrientation" />
                 </assert_contents>
-            </output>            <assert_stdout>
-                <has_text_matching expression='attr="maxmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
-                <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
-            </assert_stdout>
+            </output>
             <assert_stdout>
+                <has_text_matching expression='attr="maxmem" val0="\d+"'/>
+                <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
                 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
-            </assert_stdout>
-             <assert_stdout>
                 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
@@ -560,11 +540,6 @@
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_not_scaffolded" ftype="fasta">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
             <output name="report" file="test_03_report.txt" ftype="txt"/>
             <output name="ngs_contigs_scaffold_agp" ftype="agp">
                 <assert_contents>
@@ -585,17 +560,9 @@
             </output>
             <assert_stdout>
                 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
-            </assert_stdout>
-             <assert_stdout>
                 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
@@ -617,11 +584,6 @@
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_not_scaffolded" ftype="fasta">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
             <output name="report" file="test_04_report.txt" ftype="txt"/>
             <output name="ngs_contigs_scaffold_agp" ftype="agp">
                 <assert_contents>
@@ -642,17 +604,9 @@
             </output>
             <assert_stdout>
                 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
-            </assert_stdout>
-             <assert_stdout>
                 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
@@ -673,9 +627,43 @@
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_not_scaffolded_trimmed" ftype="fasta">
+            <output name="conflicts" ftype="txt">
+                <assert_contents>
+                    <has_text text="alignmentOrientation" />
+                </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="0" />
+                    <has_size value="311" delta="20" />
+                    <has_text text="##agp-version"/>
+                    <has_n_lines n="9"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text_matching expression='attr="maxmem" val0="\d+"'/>
+                <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
+                <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
+                <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
+                <has_text text="hybridScaffold"/>
+            </assert_stdout>
+        </test>
+        <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"/>
+            <param name="conflict_filter_sequence" value="3"/>
+            <param name="all_files" value="true"/>
+            <conditional name="configuration_options">
+                <param name="configuration" value="file"/>
+                <param name="configuration_file" value="configuration.xml"/>
+            </conditional>
+            <param name="trim_cut_sites" value="true"/>
+            <output name="ngs_contigs_scaffold_trimmed" ftype="fasta">
+                <assert_contents>
+                    <has_size value="4832591" delta="100" />
+                    <has_n_lines n="79224"/>
+                    <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
             <output name="conflicts" ftype="txt">
@@ -691,19 +679,19 @@
                     <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>
             <assert_stdout>
                 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
-            </assert_stdout>
-             <assert_stdout>
                 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
-            </assert_stdout>
-            <assert_stdout>
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
diff -r 5258e18bbe23 -r faee8629b460 macros.xml
--- a/macros.xml	Sat Feb 05 18:15:29 2022 +0000
+++ b/macros.xml	Tue Dec 13 09:26:04 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.7.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</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.