Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/3.15.5+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/3.15.5+galaxy1 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/3.15.4+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/3.15.4+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/3.15.4+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/3.15.3+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/3.15.3+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/3.15.3+galaxy0 |
spades_metaviralspades |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
spades | 3.15.5 | package |
zip | 3.0 | package |
Additional information about this tool |
#set $library = 1 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced" mkdir -p reads1 && #set file_paths1 = [] #for $input_file in $singlePaired.input1 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext #set $file_path = 'reads1/' + $fname ln -s '$input_file' '$file_path' && $file_paths1.append($file_path) #end for #else if $singlePaired.sPaired == "paired" mkdir -p paired_reads1 && #set fw_reads1 = [] #for $input_file in $singlePaired.input1 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext #set $file_path = 'paired_reads1/' + str($fname) ln -s '$input_file' '$file_path' && $fw_reads1.append($file_path) #end for #set rv_reads1 = [] #for $input_file in $singlePaired.input2 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext #set $file_path = 'paired_reads1/' + str($fname) ln -s '$input_file' '$file_path' && $rv_reads1.append($file_path) #end for #silent $fw_reads1.sort() #silent $rv_reads1.sort() #else mkdir -p paired_reads1 && #set fw_reads1 = [] #set rv_reads1 = [] #for $i, $input_file in enumerate($singlePaired.input) #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq') #set $file_path = 'paired_reads1/fw' + str($i) + '.' + $ext ln -s '$input_file.forward' '$file_path' && $fw_reads1.append($file_path) #set $file_path = 'paired_reads1/rv' + str($i) + '.' + $ext ln -s '$input_file.reverse' '$file_path' && $rv_reads1.append($file_path) #end for #end if #if $additional_reads.selector == 'true' #if $additional_reads.singlePaired.sPaired == "single" or $additional_reads.singlePaired.sPaired == "paired_interlaced" mkdir -p reads2 && #set file_paths2 = [] #for $input_file in $additional_reads.singlePaired.input1 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext #set $file_path = 'reads2/' + $fname ln -s '$input_file' '$file_path' && $file_paths2.append($file_path) #end for #else if $additional_reads.singlePaired.sPaired == "paired" mkdir -p paired_reads2 && #set fw_reads2 = [] #for $input_file in $additional_reads.singlePaired.input1 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext #set $file_path = 'paired_reads2/' + str($fname) ln -s '$input_file' '$file_path' && $fw_reads2.append($file_path) #end for #set rv_reads2 = [] #for $input_file in $additional_reads.singlePaired.input2 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext #set $file_path = 'paired_reads2/' + str($fname) ln -s '$input_file' '$file_path' && $rv_reads2.append($file_path) #end for #silent $fw_reads2.sort() #silent $rv_reads2.sort() #else mkdir -p paired_reads2 && #set fw_reads2 = [] #set rv_reads2 = [] #for $i, $input_file in enumerate($additional_reads.singlePaired.input) #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq') #set $file_path = 'paired_reads2/fw' + str($i) + '.' + $ext ln -s '$input_file.forward' '$file_path' && $fw_reads2.append($file_path) #set $file_path = 'paired_reads2/rv' + str($i) + '.' + $ext ln -s '$input_file.reverse' '$file_path' && $rv_reads2.append($file_path) #end for #end if #end if #if $arf.nanopore mkdir -p nanopore_reads && #set nanopore_reads = [] #for $i, $input_file in enumerate($arf.nanopore,1) #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = 'file' + str($i) + '.' + $ext #set $file_path = 'nanopore_reads/' + $fname ln -s '$input_file' '$file_path' && $nanopore_reads.append($file_path) #end for #end if #if $arf.pacbio mkdir -p pacbio_reads && #set pacbio_reads = [] #for $i, $input_file in enumerate($arf.pacbio,1) #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = 'file' + str($i) + '.' + $ext #set $file_path = 'pacbio_reads/' + $fname ln -s '$input_file' '$file_path' && $pacbio_reads.append($file_path) #end for #end if #if $arf.sanger mkdir -p sanger_reads && #set sanger_reads = [] #for $i, $input_file in enumerate($arf.sanger,1) #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = 'file' + str($i) + '.' + $ext #set $file_path = 'sanger_reads/' + $fname ln -s '$input_file' '$file_path' && $sanger_reads.append($file_path) #end for #end if #if $arf.trusted_contigs mkdir -p trusted_contigs && #set trusted_contigs = [] #for $i, $input_file in enumerate($arf.trusted_contigs,1) #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = 'file' + str($i) + '.' + $ext #set $file_path = 'trusted_contigs/' + $fname ln -s '$input_file' '$file_path' && $trusted_contigs.append($file_path) #end for #end if #if $arf.untrusted_contigs mkdir -p untrusted_contigs && #set untrusted_contigs = [] #for $i, $input_file in enumerate($arf.untrusted_contigs,1) #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') #set $fname = 'file' + str($i) + '.' + $ext #set $file_path = 'untrusted_contigs/' + $fname ln -s '$input_file' '$file_path' && $untrusted_contigs.append($file_path) #end for #end if #if $arf.assembly_graph mkdir -p assembly_graphs && #set assembly_graphs = [] #for $i, $input_file in enumerate($arf.assembly_graph,1) #set $ext = $input_file.ext.replace('gfa1', 'gfa') #set $fname = 'file' + str($i) + '.' + $ext #set $file_path = 'assembly_graphs/' + $fname ln -s '$input_file' '$file_path' && $assembly_graphs.append($file_path) #end for #end if export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} && ## run spades.py --metaviral $operation_mode -o 'output' -t \${GALAXY_SLOTS:-4} -m \$((\${GALAXY_MEMORY_MB:-8192}/1024)) --tmp-dir \${TMPDIR} #if $singlePaired.sPaired == "single" #for $read in $file_paths1 --s $library '${read}' #end for #else if $singlePaired.sPaired == "paired" #for $read in $fw_reads1 --${singlePaired.type_paired}-1 $library '${read}' #end for #for $read in $rv_reads1 --${singlePaired.type_paired}-2 $library '${read}' --${singlePaired.type_paired}-or $library $singlePaired.orientation #end for #else if $singlePaired.sPaired == "paired_interlaced" #for $read in $file_paths1 --${singlePaired.type_paired}-12 $library '${read}' --${singlePaired.type_paired}-or $library $singlePaired.orientation #end for #else #for $read in $fw_reads1 --${singlePaired.type_paired}-1 $library '${read}' #end for #for $read in $rv_reads1 --${singlePaired.type_paired}-2 $library '${read}' --${singlePaired.type_paired}-or $library $singlePaired.orientation #end for #end if #if $additional_reads.selector == 'true' #if $additional_reads.selector == 'true' and $additional_reads.library_number == 'false' #set $library += 1 #end if #if $additional_reads.singlePaired.sPaired == "single" #for $read in $file_paths2 --s $library '${read}' #end for #else if $additional_reads.singlePaired.sPaired == "paired" #for $read in $fw_reads2 --${additional_reads.singlePaired.type_paired}-1 $library '${read}' #end for #for $read in $rv_reads2 --${additional_reads.singlePaired.type_paired}-2 $library '${read}' --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation #end for #else if $additional_reads.singlePaired.sPaired == "paired_interlaced" #for $read in $file_paths2 --${additional_reads.singlePaired.type_paired}-12 $library '${read}' --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation #end for #else #for $read in $fw_reads2 --${additional_reads.singlePaired.type_paired}-1 $library '${read}' #end for #for $read in $rv_reads2 --${additional_reads.singlePaired.type_paired}-2 $library '${read}' --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation #end for #end if #end if ## reads #if $arf.nanopore #for $read in $nanopore_reads --nanopore $read #end for #end if #if $arf.pacbio #for $read in $pacbio_reads --pacbio $read #end for #end if #if $arf.sanger #for $read in $sanger_reads --sanger $read #end for #end if #if $arf.trusted_contigs #for $read in $trusted_contigs --trusted-contigs $read #end for #end if #if $arf.untrusted_contigs #for $read in $untrusted_contigs --untrusted-contigs $read #end for #end if #if $arf.assembly_graph #for $graph in $assembly_graphs --assembly-graph $graph #end for #end if ## parameter #if $kmer_cond.kmer_sel != 'auto' -k '$kmer_cond.manual' #end if #if $phred_offset != 'auto' --phred-offset $phred_offset #end if #for $i in $mode_sel $i #end for ## postprocessing #if 'cs' in $optional_output && test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.' #end if #if 'ss' in $optional_output && test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.' #end if #if 'corrected' in $optional_output && test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
singlePaired|input1: pl1.fq.gz singlePaired|input2: pl2.fq.gz singlePaired|sPaired: paired |
name: value name: value |
pl1.fq.gz pl2.fq.gz value |
Test-2 |
singlePaired|input1: pl1.fq.gz singlePaired|input2: pl2.fq.gz singlePaired|sPaired: paired kmer_cond|manual: 33 kmer_cond|kmer_sel: manual phred_offset: 33 optional_output: ['cn', 'cs', 'cr', 'sc', 'ss', 'l'] |
name: value name: value name: value name: value name: value |
pl1.fq.gz pl2.fq.gz value |
Test-3 |
singlePaired|input1: pl1.fq.gz singlePaired|input2: pl2.fq.gz singlePaired|sPaired: paired operation_mode: --only-assembler optional_output: l |
name: value |
pl1.fq.gz pl2.fq.gz value |
Test-4 |
singlePaired|input1: pl1.fq.gz singlePaired|input2: pl2.fq.gz singlePaired|sPaired: paired operation_mode: --only-error-correction optional_output: ['cr', 'l'] |
name: value |
pl1.fq.gz pl2.fq.gz value |