# HG changeset patch
# User bgruening
# Date 1644084861 0
# Node ID 42b12498bfa6e7d31a83633ac9b7279940e92b48
# Parent  b0c441b90e2322bccabfa9b9dc705d7a17291d5d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 25785fac3064e7def7ebccd45d452dc0b22ec89a"

diff -r b0c441b90e23 -r 42b12498bfa6 bionano_scaffold.xml
--- a/bionano_scaffold.xml	Mon Jan 17 08:14:24 2022 +0000
+++ b/bionano_scaffold.xml	Sat Feb 05 18:14:21 2022 +0000
@@ -6,7 +6,7 @@
     <expand macro="edam_ontology"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        #set RefAligner = '/usr/local/bin/RefAligner'
+        #set RefAligner = '/RefAligner/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
@@ -56,6 +56,7 @@
         $zip_file
         -o ./
         #if $trim_cut_sites
+            && export PATH=/opt/conda/bin/:\$PATH
             && python '$__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 
@@ -472,7 +473,6 @@
             </output>            
             <output name="results" ftype="zip">
                 <assert_contents>
-                    <!--<has_size value="4231746" delta="300" />-->
                     <has_archive_member path=".*/status.txt"/>
                 </assert_contents>
             </output>
@@ -540,7 +540,6 @@
             </assert_stdout>
             <assert_stdout>
                 <has_text text="hybridScaffold"/>
-                <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/-->
             </assert_stdout>
         </test>
         <test expect_num_outputs="6">
@@ -581,7 +580,6 @@
             </output>            
             <output name="results" ftype="zip">
                 <assert_contents>
-                    <!--<has_size value="4231908" delta="300" />-->
                     <has_archive_member path=".*/status.txt"/>
                 </assert_contents>
             </output>
diff -r b0c441b90e23 -r 42b12498bfa6 macros.xml
--- a/macros.xml	Mon Jan 17 08:14:24 2022 +0000
+++ b/macros.xml	Sat Feb 05 18:14:21 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.6.1</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@TOOL_VERSION@">3.7.0</token>
+    <token name="@VERSION_SUFFIX@">0</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.
@@ -12,7 +12,6 @@
 For the latest supported Bionano software, visit Bionano Support
 https://bionanogenomics.com/support/
     </token>
-
     <xml name="edam_ontology">
         <edam_topics>
             <edam_topic>topic_0196</edam_topic>
@@ -23,7 +22,7 @@
     </xml>
     <xml name="requirements">
         <requirements>
-            <container type="docker">quay.io/galaxy/bionano-docker-scaffold:1.6.01-bio</container>
+            <container type="docker">quay.io/galaxy/bionano-docker-scaffold:1.7.0-bio</container>
         </requirements>
     </xml>
     <macro name="sanitize_string" >