Repository revision
11:3371c5bdc17a

Repository 'bionano_scaffold'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold

Bionano Hybrid Scaffold tool metadata
Miscellaneous
automates the scaffolding process
bionano_scaffold
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3
3.7.0+galaxy3
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy2
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy1
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.6.1+galaxy3
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.6.1+galaxy2
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.6.1+galaxy1
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.6.1+galaxy0
bionano_scaffold
Requirements (dependencies defined in the <requirements> tag set)
No requirements defined
Additional information about this tool
#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
        cp '${ngs_fasta}' ./ngs.fasta
        && cp '${bionano_cmap}' ./bionano.cmap
        && export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024))
        ## return max out of  GALAXY_SLOTS and 2 --> use a minimum 2 slots
        && export SLOTS=\$(( \${GALAXY_SLOTS:-2} > 2 ? \${GALAXY_SLOTS:-2} : 2 ))
        #if $configuration_options.configuration == 'vgp'
            && cp '${vgp_mode}' ./config.xml
            && sed -i "s|__MEMORY__|\$GALAXY_MEMORY_GB|" ./config.xml
            && sed -i "s|__CORES__|\$SLOTS|" ./config.xml
        #else
            && cp '${configuration_file}' ./config.xml
            && sed -i "s|attr=\"maxmem\" val0=.* display|attr=\"maxmem\" val0=\"\$GALAXY_MEMORY_GB\" display|" ./config.xml
            && sed -i "s|attr=\"maxthreads\" val0=.* display|attr=\"maxthreads\" val0=\"\$SLOTS\" display|" ./config.xml
            && sed -i "s|attr=\"maxvirtmem\" val0=.*/>|attr=\"maxvirtmem\" val0=\"\$GALAXY_MEMORY_GB\"/>|" ./config.xml
            && sed -i "s|attr=\"insertThreads\" val0=.*/>|attr=\"insertThreads\" val0=\"\$SLOTS\"/>|" ./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}'
        #else
            -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 ./
        #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
        ## the next lines are required because the XXXX_cut.txt file is not always generated
        && touch hybrid_scaffolds/temp_cut.txt
        && cat hybrid_scaffolds/*cut.txt > hybrid_scaffolds/keys.txt
        
None
False
Functional tests
name inputs outputs required files
Test-1 ngs_fasta: assembly.fasta.gz
bionano_cmap: colormap_assembly.cmap
configuration_options|configuration_file: configuration.xml
configuration_options|configuration: file
conflict_filter_genome: 3
conflict_filter_sequence: 3
zip_file: True
trim_cut_sites: False
name: value
name: value
name: value
name: value
name: value
assembly.fasta.gz
colormap_assembly.cmap
configuration.xml
value
Test-2 ngs_fasta: assembly.fasta.gz
bionano_cmap: colormap_assembly.cmap
configuration_options|configuration_file: configuration.xml
configuration_options|configuration: file
conflict_filter_genome: 2
conflict_filter_sequence: 2
trim_cut_sites: False
name: value
name: value
name: value
name: value
assembly.fasta.gz
colormap_assembly.cmap
configuration.xml
value
Test-3 ngs_fasta: assembly.fasta.gz
bionano_cmap: colormap_assembly.cmap
configuration_options|configuration_file: configuration.xml
configuration_options|configuration: file
conflict_filter_genome: 2
conflict_filter_sequence: 3
zip_file: True
trim_cut_sites: False
name: value
name: value
name: value
name: value
name: value
assembly.fasta.gz
colormap_assembly.cmap
configuration.xml
value
Test-4 ngs_fasta: assembly.fasta.gz
bionano_cmap: colormap_assembly.cmap
configuration_options|enzyme: BspQI
configuration_options|configuration: vgp
conflict_filter_genome: 2
conflict_filter_sequence: 3
zip_file: True
trim_cut_sites: False
name: value
name: value
name: value
name: value
name: value
assembly.fasta.gz
colormap_assembly.cmap
value
Test-5 ngs_fasta: assembly.fasta.gz
bionano_cmap: colormap_assembly.cmap
configuration_options|configuration_file: configuration.xml
configuration_options|configuration: file
conflict_filter_genome: 3
conflict_filter_sequence: 3
trim_cut_sites: True
name: value
name: value
name: value
name: value
assembly.fasta.gz
colormap_assembly.cmap
configuration.xml
value
Test-6 ngs_fasta: assembly.fasta.gz
bionano_cmap: colormap_assembly.cmap
configuration_options|configuration_file: configuration.xml
configuration_options|configuration: file
conflict_filter_genome: 3
conflict_filter_sequence: 3
all_files: True
trim_cut_sites: True
name: value
name: value
name: value
name: value
name: value
name: value
name: value
assembly.fasta.gz
colormap_assembly.cmap
configuration.xml
value