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1 <tool id="srst2v2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0">
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2 <requirements>
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3 <requirement type="package" version="0.2.0">srst2</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 #if $paired_conditional.sPaired == "paired"
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7 ln -s $paired_conditional.fastq1 sample_1.fastq;
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8 ln -s $paired_conditional.fastq2 sample_2.fastq;
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9 #end if
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10
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11 srst2
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12
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13 #if $paired_conditional.sPaired == "single"
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14 --input_se $paired_conditional.fastq1
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15 #else if $paired_conditional.sPaired == "paired"
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16 --input_pe sample_1.fastq sample_2.fastq
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17 #end if
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18
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19 --output srst2out
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20 --save_scores
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21 --mlst_definitions "$mlst_definitions"
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22 --mlst_db "$mlst_db"
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23 --mlst_delimiter $mlstdelim
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24 --mlst_max_mismatch $mlst_max_mismatch
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25
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26 ]]></command>
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27 <inputs>
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28 <conditional name="paired_conditional">
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29 <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?">
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30 <option value="single">Single-end</option>
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31 <option value="paired">Paired-end</option>
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32 </param>
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33 <when value="single">
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34 <param name="fastq1" type="data" format="fastq" label="FASTQ file" help="FASTQ" />
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35 </when>
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36 <when value="paired">
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37 <param name="fastq1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ" />
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38 <param name="fastq2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ" />
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39 </when>
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40 </conditional>
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41
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42 <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
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43 <param type="data" name="mlst_definitions" label="ST definitions for MLST scheme" format="tabular" />
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44 <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default '_')" />
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45 <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read for MLST allele calling (default 10)" />
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46 </inputs>
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47
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48 <outputs>
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49 <data format="txt" label="Scores" name="scores" from_work_dir="*.scores"/>
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50 <data format="bam" label="bam alignment" name="bam" from_work_dir="*.sorted.bam"/>
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51 <data format="pileup" label="pileup" name="pileup" from_work_dir="*.pileup"/>
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52 <data format="txt" label="Alleles" name="alleles" from_work_dir="*results.txt"/>
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53 </outputs>
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54
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55 <help><![CDATA[
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56
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57 SRST2 - Short Read Sequence Typer (v2)
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58
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59 This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
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60
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61
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62
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63 optional arguments:
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64 -h, --help show this help message and exit
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65 --version show program's version number and exit
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66 --input_se INPUT_SE
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67 Single end read file(s) for analysing (may be gzipped)
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68 --input_pe INPUT_PE
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69 Paired end read files for analysing (may be gzipped)
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70 --merge_paired Switch on if all the input read sets belong to a
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71 single sample, and you want to merge their data to get
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72 a single result
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73 --forward FORWARD Designator for forward reads (only used if NOT in
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74 MiSeq format sample_S1_L001_R1_001.fastq.gz; otherwise
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75 default is _1, i.e. expect forward reads as
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76 sample_1.fastq.gz)
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77 --reverse REVERSE Designator for reverse reads (only used if NOT in
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78 MiSeq format sample_S1_L001_R2_001.fastq.gz; otherwise
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79 default is _2, i.e. expect forward reads as
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80 sample_2.fastq.gz
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81 --read_type READ_TYPE
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82 Read file type (for bowtie2; default is q=fastq; other
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83 options: qseq=solexa, f=fasta).
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84 --mlst_db MLST_DB Fasta file of MLST alleles (optional)
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85 --mlst_delimiter MLST_DELIMITER
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86 Character(s) separating gene name from allele number
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87 in MLST database (default "-", as in arcc-1)
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88 --mlst_definitions MLST_DEFINITIONS
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89 ST definitions for MLST scheme (required if mlst_db
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90 supplied and you want to calculate STs)
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91 --mlst_max_mismatch MLST_MAX_MISMATCH
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92 Maximum number of mismatches per read for MLST allele
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93 calling (default 10)
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94 --gene_db GENE_DB
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95 Fasta file/s for gene databases (optional)
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96 --no_gene_details Switch OFF verbose reporting of gene typing
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97 --gene_max_mismatch GENE_MAX_MISMATCH
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98 Maximum number of mismatches per read for gene
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99 detection and allele calling (default 10)
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100 --min_coverage MIN_COVERAGE
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101 Minimum %coverage cutoff for gene reporting (default
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102 90)
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103 --max_divergence MAX_DIVERGENCE
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104 Maximum %divergence cutoff for gene reporting (default
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105 10)
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106 --min_depth MIN_DEPTH
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107 Minimum mean depth to flag as dubious allele call
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108 (default 5)
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109 --min_edge_depth MIN_EDGE_DEPTH
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110 Minimum edge depth to flag as dubious allele call
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111 (default 2)
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112 --prob_err PROB_ERR Probability of sequencing error (default 0.01)
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113 --truncation_score_tolerance TRUNCATION_SCORE_TOLERANCE
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114 % increase in score allowed to choose non-truncated
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115 allele
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116 --stop_after STOP_AFTER
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117 Stop mapping after this number of reads have been
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118 mapped (otherwise map all)
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119 --other OTHER
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120 Other arguments to pass to bowtie2 (must be escaped,
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121 e.g. "\\--no-mixed".)
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122 --max_unaligned_overlap MAX_UNALIGNED_OVERLAP
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123 Read discarded from alignment if either of its ends
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124 has unaligned overlap with the reference that is
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125 longer than this value (default 10)
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126 --mapq MAPQ Samtools -q parameter (default 1)
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127 --baseq BASEQ Samtools -Q parameter (default 20)
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128 --samtools_args SAMTOOLS_ARGS
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129 Other arguments to pass to samtools mpileup (must be
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130 escaped, e.g. "\\-A").
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131 --output OUTPUT Prefix for srst2 output files
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132 --log Switch ON logging to file (otherwise log to stdout)
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133 --save_scores Switch ON verbose reporting of all scores
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134 --report_new_consensus
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135 If a matching alleles is not found, report the
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136 consensus allele. Note, only SNP differences are
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137 considered, not indels.
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138 --report_all_consensus
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139 Report the consensus allele for the most likely
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140 allele. Note, only SNP differences are considered, not
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141 indels.
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142 --use_existing_bowtie2_sam
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143 Use existing SAM file generated by Bowtie2 if
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144 available, otherwise they will be generated
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145 --use_existing_pileup
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146 Use existing pileups if available, otherwise they will
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147 be generated
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148 --use_existing_scores
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149 Use existing scores files if available, otherwise they
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150 will be generated
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151 --keep_interim_alignment
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152 Keep interim files (sam & unsorted bam), otherwise
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153 they will be deleted after sorted bam is created
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154 --threads THREADS Use multiple threads in Bowtie and Samtools
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155 --prev_output PREV_OUTPUT
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156 SRST2 results files to compile (any new results from
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157 this run will also be incorporated)
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158
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159
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160 ]]></help>
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161
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162
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163 <citations>
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164 <citation type="bibtex">
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165 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
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166 title={SRST2: Rapid genomic surveillance for public health and hospital microbiology labs},
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167 url={https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0090-6},
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168 journal={Genome Medicine}, publisher={BioMed Central},
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169 author={Pope, Bernard J and Dashnow, Harriet and Zobel, Justin and Holt, Kathryn E and Raven, Lesley-Ann and Schultz, Mark B and Inouye, Michael and Tomita, Takehiro},
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170 year={2014}, month={Nov}} ,
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171 }</citation>
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172 </citations>
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173 </tool>
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