# HG changeset patch
# User bgruening
# Date 1621286000 0
# Node ID 9bd94d9a1b2eeaccc9145f782d98c330dcfe6361
# Parent fec6a0b53189a18d81e7812e7d7a2d63080cc7ff
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty"
diff -r fec6a0b53189 -r 9bd94d9a1b2e bionano_scaffold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bionano_scaffold.xml Mon May 17 21:13:20 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
+ $zip_file
+ -o ./
+ ##;
+ ##sleep 1000000
+
+ ]]>
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+ #end if
+ ]]>
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+ VGP mode
+ Select a configuration file
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+ No filter
+ Cut contig at conflict
+ Exclude conflicting contig
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+ No filter
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+ Exclude conflicting contig
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diff -r fec6a0b53189 -r 9bd94d9a1b2e bionano_scaffold_edited.xml
--- a/bionano_scaffold_edited.xml Mon May 17 15:07:05 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,617 +0,0 @@
-
- automates the scaffolding process
-
- macros.xml
-
- perl /HybridScaffold/hybridScaffold.pl --version
- |attr="maxvirtmem" val0="$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
-
- ]]>
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- #end if
- ]]>
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- Exclude conflicting contig
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diff -r fec6a0b53189 -r 9bd94d9a1b2e bionano_scaffold_edited_test_report.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bionano_scaffold_edited_test_report.html Mon May 17 21:13:20 2021 +0000
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+ Test Results (powered by Planemo)
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\ No newline at end of file
diff -r fec6a0b53189 -r 9bd94d9a1b2e macros.xml
--- a/macros.xml Mon May 17 15:07:05 2021 +0000
+++ b/macros.xml Mon May 17 21:13:20 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
diff -r fec6a0b53189 -r 9bd94d9a1b2e test-data/foo.zip
Binary file test-data/foo.zip has changed
diff -r fec6a0b53189 -r 9bd94d9a1b2e test-data/foo2.zip
Binary file test-data/foo2.zip has changed