Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/srst2/srst2/0.2.0+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/srst2/srst2/0.2.0+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/srst2/srst2/0.2.0+galaxy0 |
srst2 |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
samtools | 0.1.18 | package |
srst2 | 0.2.0 | package |
Additional information about this tool |
#if $input.selector == "single" #set ext=$input.single_input.datatype.file_ext ln -s $input.single_input './input_read1.$ext' && #else if $input.selector == "paired" #set ext_1=$input.paired_input1.datatype.file_ext #set ext_2=$input.paired_input2.datatype.file_ext ln -s $input.paired_input1 './input_read1.$ext_1' && ln -s $input.paired_input2 './input_read2.$ext_2' && #end if #for $i, $s in enumerate($prev_output) #if $s ln -s $s './$i-prev_output.txt' && #end if #end for #if $use_gene_db.selector == "yes" #for $i, $s in enumerate($use_gene_db.gene_db) #if $s ln -s $s './$i-gene_db.fasta' && #end if #end for #end if #if $use_mlst_db.selector == "yes" #set ext_3=$use_mlst_db.mlst_definitions.datatype.file_ext ln -s $use_mlst_db.mlst_db './mlst_db.fasta' && ln -s $use_mlst_db.mlst_definitions './mlst_definitions.$ext_3' && #end if srst2 #if $input.selector == "single" --input_se './input_read1.$ext' --read_type ${input.read_type} #else if $input.selector == "paired" --input_pe './input_read1.$ext_1' './input_read2.$ext_2' $input.merge_paired --forward _read1 --reverse _read2 --read_type ${input.read_type} #end if #if $use_mlst_db.selector == "yes" --mlst_db './mlst_db.fasta' --mlst_definitions './mlst_definitions.$ext_3' --mlst_delimiter '$use_mlst_db.mlst_delimiter' --mlst_max_mismatch $use_mlst_db.mlst_max_mismatch --min_depth $use_mlst_db.min_depth --min_edge_depth $use_mlst_db.min_edge_depth #end if #if $use_gene_db.selector == "yes" --gene_db #for $i, $s in enumerate($use_gene_db.gene_db) #if $s '$i-gene_db.fasta' #end if #end for $use_gene_db.no_gene_details --gene_max_mismatch $use_gene_db.gene_max_mismatch --min_coverage $use_gene_db.min_coverage --max_divergence $use_gene_db.max_divergence #end if --prob_err $prob_err #if $truncation_score_tolerance --truncation_score_tolerance $truncation_score_tolerance #end if #if $stop_after --stop_after $stop_after #end if --max_unaligned_overlap $max_unaligned_overlap --mapq $mapq --baseq $baseq --output 'output' #if $prev_output --prev_output #for $i, $s in enumerate($prev_output) #if $s '$i-prev_output.txt' #end if #end for #end if #if 'log' in str($output_files_selector) --log #end if #if 'save_scores' in str($output_files_selector) --save_scores #end if #if 'report_new_consensus' in str($output_files_selector) --report_new_consensus #end if #if 'report_all_consensus' in str($output_files_selector) --report_all_consensus #end if #if 'keep_interim_alignment' in str($output_files_selector) --keep_interim_alignment #end if ## |true here is added in order not to search for a file that is not produced at all, such that if the user provided no gene/MLST databases or there are no outputs found, the tool will run successfully and only notify the user that no outputs are found #if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes" && mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true #end if #if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details && mkdir -p geneTypingOutput/ geneTypingOutputFull/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutputFull | true #end if #if 'save_scores' in str($output_files_selector) && mkdir -p scoresOutput/ && cp *.scores scoresOutput | true #end if #if $input.selector == "single" or $input.selector == "paired" && mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments | true && mkdir -p samtoolsPileup/ && cp output__input.*.pileup samtoolsPileup | true #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input|paired_input1: ERR024070_1_reduced_forward_reads.fastqsanger.gz input|paired_input2: ERR024070_2_reduced_reverse_reads.fastqsanger.gz input|merge_paired: False input|read_type: q input|selector: paired use_mlst_db|mlst_db: Escherichia_coli1R.fasta use_mlst_db|mlst_definitions: profiles_csv use_mlst_db|mlst_delimiter: _ use_mlst_db|mlst_max_mismatch: 10 use_mlst_db|min_depth: 5 use_mlst_db|min_edge_depth: 2 use_mlst_db|selector: yes use_gene_db|gene_db: ARGannotR.fasta use_gene_db|no_gene_details: True use_gene_db|gene_max_mismatch: 10 use_gene_db|min_coverage: 90 use_gene_db|max_divergence: 10 use_gene_db|selector: yes output_files_selector: ['log', 'save_scores', 'report_new_consensus', 'report_all_consensus'] prob_err: 0.01 max_unaligned_overlap: 10 mapq: 1 baseq: 20 |
name: value name: value name: value name: value |
ERR024070_1_reduced_forward_reads.fastqsanger.gz ERR024070_2_reduced_reverse_reads.fastqsanger.gz Escherichia_coli1R.fasta profiles_csv ARGannotR.fasta value |
Test-2 |
input|paired_input1: ERR024070_1_reduced_forward_reads.fastqsanger.gz input|paired_input2: ERR024070_2_reduced_reverse_reads.fastqsanger.gz input|merge_paired: False input|read_type: q input|selector: paired use_mlst_db|selector: no use_gene_db|selector: no output_files_selector: ['log', 'save_scores', 'report_new_consensus', 'report_all_consensus'] prob_err: 0.01 max_unaligned_overlap: 10 mapq: 1 baseq: 20 |
name: value name: value name: value |
ERR024070_1_reduced_forward_reads.fastqsanger.gz ERR024070_2_reduced_reverse_reads.fastqsanger.gz value |