--- a/bionano_scaffold.xml	Sun May 23 17:23:03 2021 +0000
+++ b/bionano_scaffold.xml	Tue May 25 20:12:52 2021 +0000
@@ -7,6 +7,8 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         #set RefAligner = '/usr/local/bin/RefAligner'
+        #set output_file_NCBI = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta'
+        #set output_file_not_scaffolded = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta'
         ## softlinks do not work
         cp '${ngs_fasta}' ./ngs.fasta
         && cp '${bionano_cmap}' ./bionano.cmap
@@ -33,8 +35,7 @@
         -r $RefAligner
         #if $conflict_resolution
             -M '${conflict_resolution}'
-        #end if
-        #if not $conflict_resolution
+        #else
             -B $conflict_filter_genome
             -N $conflict_filter_sequence
         #end if
@@ -54,7 +55,10 @@
         -f
         $zip_file
         -o ./
-
+        && cat $output_file_NCBI $output_file_not_scaffolded > total_contigs_raw.fasta
+        #if $trim_cut_sites
+            && python '$__tool_directory__/remove_fake_cut_sites.py' 'total_contigs_raw.fasta' 'total_contigs_trimmed.fasta' 'output.log'
+        #end if        
     ]]>    </command>
     <configfiles>
         <configfile name="vgp_mode"><![CDATA[
@@ -70,7 +74,7 @@
                         <flag attr="RAmem" val0="3" val1="1"/>
                     </global>
                     <fasta2cmap>
-                        <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
+                        <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Available enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
                         <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
                         <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/>
                         <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/>
@@ -384,6 +388,7 @@
             <option value="3">Exclude conflicting contig</option>
         </param>
         <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." />
         <!-- 
         
         Those options have been disabled because the Docker container doesn't include the required packages
@@ -415,16 +420,22 @@
         -->
     </inputs>
     <outputs>
-        <data name="ngs_contigs_scaffold_fasta" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta" label="${tool.name} on ${on_string}: NGScontigs hybrid scaffold (fasta)"/>
-        <data name="ngs_contigs_scaffold_agp" format="txt" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: NGScontigs hybrid scaffold (agp)"/>
-        <data name="ngs_contigs_scaffold_gap" format="txt" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.gap" label="${tool.name} on ${on_string}: NGScontigs hybrid scaffold (gap)"/>
+        <data name="ngs_contigs" format="fasta" from_work_dir="total_contigs_raw.fasta" label="${tool.name} on ${on_string}: NGScontigs">
+            <filter>trim_cut_sites == False</filter>
+        </data>
+        <data name="ngs_contigs_trimmed" format="fasta" from_work_dir="total_contigs_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs trimmed">
+            <filter>trim_cut_sites</filter>
+        </data>
+        <data name="ngs_contigs_trimmed_report" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: NGScontigs trimmed log">
+            <filter>trim_cut_sites</filter>
+        </data>
         <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${tool.name} on ${on_string}: hybrid scaffold report"/>
         <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">
             <filter>zip_file</filter>
         </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="3">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="3"/>
@@ -434,13 +445,12 @@
                 <param name="configuration_file" value="configuration.xml"/>
             </conditional>
             <param name="zip_file" value="true"/>
-            <output name="ngs_contigs_scaffold_fasta" ftype="fasta">
+            <param name="trim_cut_sites" value="false"/>
+            <output name="ngs_contigs" ftype="fasta">
                 <assert_contents>
                     <has_size value="4753369" delta="300" />
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_scaffold_agp" file="test_01.agp" ftype="txt"/>
-            <output name="ngs_contigs_scaffold_gap" file="test_01.gap" ftype="txt"/>
             <output name="report" file="test_01_report.txt" ftype="txt"/>
             <output name="results" ftype="zip">
                 <assert_contents>
@@ -464,24 +474,23 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="2">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="2"/>
             <param name="conflict_filter_sequence" value="2"/>
+            <param name="trim_cut_sites" value="false"/>
             <conditional name="configuration_options">
                 <param name="configuration" value="file"/>
                 <param name="configuration_file" value="configuration.xml"/>
             </conditional>
-            <output name="ngs_contigs_scaffold_fasta" ftype="fasta">
+            <output name="ngs_contigs" ftype="fasta">
                 <assert_contents>
                     <has_size value="4753369" delta="100" />
                     <has_n_lines n="2"/>
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_scaffold_agp" file="test_02.agp" ftype="txt"/>
-            <output name="ngs_contigs_scaffold_gap" file="test_02.gap" ftype="txt"/>
             <output name="report" file="test_02_report.txt" ftype="txt"/>
             <assert_stdout>
                 <has_text text='attr="maxmem" val0="8"'/>
@@ -500,7 +509,7 @@
                 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/-->
             </assert_stdout>
         </test>
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="3">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="2"/>
@@ -510,15 +519,14 @@
                 <param name="configuration_file" value="configuration.xml"/>
             </conditional>
             <param name="zip_file" value="true"/>
-            <output name="ngs_contigs_scaffold_fasta" ftype="fasta">
+            <param name="trim_cut_sites" value="false"/>
+            <output name="ngs_contigs" ftype="fasta">
                 <assert_contents>
                     <has_size value="4753369" delta="100" />
                     <has_n_lines n="2"/>
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_scaffold_agp" file="test_03.agp" ftype="txt"/>
-            <output name="ngs_contigs_scaffold_gap" file="test_03.gap" ftype="txt"/>
             <output name="report" file="test_03_report.txt" ftype="txt"/>
             <output name="results" ftype="zip">
                 <assert_contents>
@@ -542,7 +550,7 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="3">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="2"/>
@@ -552,15 +560,14 @@
                 <param name="enzyme" value="BspQI"/>
             </conditional>
             <param name="zip_file" value="true"/>
-            <output name="ngs_contigs_scaffold_fasta" ftype="fasta">
+            <param name="trim_cut_sites" value="false"/>
+            <output name="ngs_contigs" ftype="fasta">
                 <assert_contents>
                     <has_size value="4753369" delta="100" />
                     <has_n_lines n="2"/>
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_scaffold_agp" file="test_04.agp" ftype="txt"/>
-            <output name="ngs_contigs_scaffold_gap" file="test_04.gap" ftype="txt"/>
             <output name="report" file="test_04_report.txt" ftype="txt"/>
             <output name="results" ftype="zip">
                 <assert_contents>
@@ -583,6 +590,43 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
+        <test expect_num_outputs="3">
+            <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"/>
+            <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_trimmed" ftype="fasta">
+                <assert_contents>
+                    <has_size value="4832591" delta="300" />
+                </assert_contents>
+            </output>
+            <output name="ngs_contigs_trimmed_report" ftype="txt">
+                <assert_contents>
+                    <has_size value="0" />
+                </assert_contents>
+            </output>
+            <output name="report" file="test_05_report.txt" ftype="txt"/>
+            <assert_stdout>
+                <has_text text='attr="maxmem" val0="8"'/>
+            </assert_stdout>
+            <assert_stdout>
+                <has_text text='attr="maxthreads" val0="1"'/>
+            </assert_stdout>
+            <assert_stdout>
+                <has_text text='attr="insertThreads" val0="1"'/>
+            </assert_stdout>
+             <assert_stdout>
+                <has_text text='attr="maxvirtmem" val0="8"'/>
+            </assert_stdout>
+            <assert_stdout>
+                <has_text text="hybridScaffold"/>
+            </assert_stdout>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark