Repository revision
3:f995ba9f1caa

Repository 'srst2'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/srst2

SRST2 tool metadata
Miscellaneous
SRST2
Short Read Sequence Typing for Bacterial Pathogens
srst2
toolshed.g2.bx.psu.edu/repos/iuc/srst2/srst2/0.2.0+galaxy2
0.2.0+galaxy2
srst2 --version
True
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
    
None
False
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