# HG changeset patch
# User bgruening
# Date 1621286694 0
# Node ID 13529dc38551cd5bf7fa7c6c63e9b56865a5083b
# Parent 33ce8b6ec877530f3966315c9a87b4713d0fa2e1
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit b3f6ea67abe31b523fd9132c6b2d9d8a2d3d86f7"
diff -r 33ce8b6ec877 -r 13529dc38551 bionano_scaffold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bionano_scaffold.xml Mon May 17 21:24:54 2021 +0000
@@ -0,0 +1,622 @@
+
+ automates the scaffolding process
+
+ macros.xml
+
+
+
+ perl /HybridScaffold/hybridScaffold.pl --version
+ |attr="maxvirtmem" val0="$cores"/>|' ./config.xml
+ && sed -i 's|attr="insertThreads" val0=.*/>|attr="insertThreads" val0="$cores"/>|' ./config.xml
+ #end if
+ ## output the configuration file on stdout
+ && cat ./config.xml
+ && perl '/HybridScaffold/hybridScaffold.pl'
+ -n ./ngs.fasta
+ -b ./bionano.cmap
+ -c ./config.xml
+ -r $RefAligner
+ #if $conflict_resolution
+ -M '${conflict_resolution}'
+ #end if
+ #if not $conflict_resolution
+ -B $conflict_filter_genome
+ -N $conflict_filter_sequence
+ #end if
+ ##$align_molecules_options.align_molecules
+ ###if $align_molecules_options.align_molecules
+ ## -m $align_molecules_options.bionano_molecules
+ ## -q '${align_molecules_options.optarguments_xml}'
+ ## -p ##/home/bionano/tools/pipeline/1.0/Pipeline/1.0/
+ ###end if
+ ##$quimeric_quality_options.quimeric_quality
+ ###if $quimeric_quality_options.quimeric_quality
+ ## -m $align_molecules_options.bionano_molecules
+ ## #if $quimeric_quality_conditional.noise_parameter
+ ## -e '${quimeric_quality_conditional.noise_parameter}'
+ ## #end if
+ ###end if
+ -f
+ $zip_file
+ -o ./
+ ##;
+ ##sleep 1000000
+
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ #end if
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ zip_file
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 33ce8b6ec877 -r 13529dc38551 bionano_scaffold_edited.xml
--- a/bionano_scaffold_edited.xml Mon May 17 15:05:48 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,617 +0,0 @@
-
- automates the scaffolding process
-
- macros.xml
-
-
-
- perl /HybridScaffold/hybridScaffold.pl --version
- |attr="maxvirtmem" val0="$cores"/>|' ./config.xml
- && sed -i 's|attr="insertThreads" val0=.*/>|attr="insertThreads" val0="$cores"/>|' ./config.xml
- #end if
- ## output the configuration file on stdout
- && cat ./config.xml
- && perl '/HybridScaffold/hybridScaffold.pl'
- -n ./ngs.fasta
- -b ./bionano.cmap
- -c ./config.xml
- -r $RefAligner
- #if $conflict_resolution
- -M '${conflict_resolution}'
- #end if
- #if not $conflict_resolution
- -B $conflict_filter_genome
- -N $conflict_filter_sequence
- #end if
- ##$align_molecules_options.align_molecules
- ###if $align_molecules_options.align_molecules
- ## -m $align_molecules_options.bionano_molecules
- ## -q '${align_molecules_options.optarguments_xml}'
- ## -p ##/home/bionano/tools/pipeline/1.0/Pipeline/1.0/
- ###end if
- ##$quimeric_quality_options.quimeric_quality
- ###if $quimeric_quality_options.quimeric_quality
- ## -m $align_molecules_options.bionano_molecules
- ## #if $quimeric_quality_conditional.noise_parameter
- ## -e '${quimeric_quality_conditional.noise_parameter}'
- ## #end if
- ###end if
- -f
- $zip_file
- -o ./
- ##;
- ##sleep 1000000
-
- ]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- #end if
- ]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- zip_file
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff -r 33ce8b6ec877 -r 13529dc38551 macros.xml
--- a/macros.xml Mon May 17 15:05:48 2021 +0000
+++ b/macros.xml Mon May 17 21:24:54 2021 +0000
@@ -1,8 +1,20 @@
3.6.1
galaxy0
+
+Bionano Genomics has agreed to provide the licensed Bionano Solve
+software to enable the VGP to package the software in a container.
+Bionanno Solve as shipped in this container may not be the latest and
+may not run efficiently on non-validated hardware. Hence, it is not
+supported by Bionano Genomics. Any questions concerning this version
+should be passed to the VGP (https://github.com/VGP/vgp-assembly/issues)
+or Galaxy community (https://help.galaxyproject.org).
+For the latest supported Bionano software, visit Bionano Support
+https://bionanogenomics.com/support/
+
+
-
+
topic_0196