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author estrain
date Sun, 03 Dec 2017 13:28:11 -0500
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1 <tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0">
2 <requirements>
3 <requirement type="package" version="0.2.0">srst2</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 #if $paired_conditional.sPaired == "paired"
7 ln -s $paired_conditional.fastq1 sample_1.fastq;
8 ln -s $paired_conditional.fastq2 sample_2.fastq;
9 #end if
10
11 srst2
12
13 #if $paired_conditional.sPaired == "single"
14 --input_se $paired_conditional.fastq1
15 #else if $paired_conditional.sPaired == "paired"
16 --input_pe sample_1.fastq sample_2.fastq
17 #end if
18
19 --output srst2out
20 --save_scores
21
22 #if $job_type.job == "mlst"
23 --mlst_definitions $job_type.mlst_definitions
24 --mlst_db $job_type.mlst_db
25 --mlst_delimiter $job_type.mlstdelim
26 --mlst_max_mismatch $job_type.mlst_max_mismatch
27 #else if $job_type.job == "gene"
28 --gene_db $job_type.genedb
29 --gene_max_mismatch $job_type.gene_max_mismatch
30 #end if
31
32 #if $options.select == "advanced"
33 #if $options.min_coverage
34 --min_coverage $options.min_coverage
35 #end if
36 #if $options.max_divergence
37 --max_divergence $options.max_divergence
38 #end if
39 #if $options.min_depth
40 --min_depth $options.min_depth
41 #end if
42 #if $options.min_edge_depth
43 --min_edge_depth $options.min_edge_depth
44 #end if
45 #if $options.prob_err
46 --prob_err $options.prob_err
47 #end if
48 #if $options.stop_after
49 --stop_after $options.stop_after
50 #end if
51 --other "'-p \${GALAXY_SLOTS:-1}
52 #if $options.maxins
53 --maxins $options.maxins
54 --minins $options.minins
55 #end if
56 '"
57 #if $options.mapq
58 --mapq $options.mapq
59 #end if
60 #if $options.baseq
61 --baseq $options.baseq
62 #end if
63 #else
64 --other "'-p \${GALAXY_SLOTS:-1}'"
65 #end if
66
67 #if $job_type.job == "mlst"
68 ; python $__tool_directory__/scoreProfiles.py --mlst_definitions $job_type.mlst_definitions --profile_cov $job_type.profile_cov --profile_max_mismatch $job_type.profile_max_mismatch --output srst2.pscores
69 #end if
70
71 ]]></command>
72 <inputs>
73 <conditional name="paired_conditional">
74 <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?">
75 <option value="single">Single-end</option>
76 <option value="paired">Paired-end</option>
77 </param>
78 <when value="single">
79 <param name="fastq1" type="data" format="fastq" label="FASTQ file" help="FASTQ" />
80 </when>
81 <when value="paired">
82 <param name="fastq1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ" />
83 <param name="fastq2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ" />
84 </when>
85 </conditional>
86
87 <conditional name="job_type">
88 <param name="job" type="select" label="MLST or Gene Presence/Absence?">
89 <option value="mlst">MLST</option>
90 <option value="gene">Gene</option>
91 </param>
92 <when value="mlst">
93 <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
94 <param type="data" name="mlst_definitions" label="ST definitions for MLST scheme" format="tabular" />
95 <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default &apos;_&apos;)" />
96 <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read" />
97 <param type="float" name="profile_max_mismatch" value="1" format="txt" label="Maximum number of mismatches for reporting ST profile" />
98 <param type="float" name="profile_cov" value="98" format="txt" label="Minimum mean % coverage for reporting ST profile" />
99
100 </when>
101 <when value="gene">
102 <param name="genedb" type="data" format="fasta" label="Fasta file for gene database" />
103 <param name="gene_max_mismatch" type="integer" value="10" format="txt" label="Maximum number of mistaches per read (default 10)" />
104 </when>
105 </conditional>
106
107 <conditional name="options">
108 <param name="select" type="select" label="Options Type">
109 <option value="basic">Basic</option>
110 <option value="advanced">Advanced</option>
111 </param>
112 <when value="advanced">
113 <param name="min_coverage" type="integer" label="Minimum %coverage cutoff for gene reporting" value="90"/>
114 <param name="max_divergence" type="integer" label="Maximum %divergence cutoff for gene reporting" value="10"/>
115 <param name="min_depth" type="integer" label="Minimum mean depth to flag as dubious allele call" value="5"/>
116 <param name="min_edge_depth" type="integer" label="Minimum edge depth to flag as dubious allele call" value="2"/>
117 <param name="prob_err" type="float" label="Probability of sequencing error" value="0.01"/>
118 <param name="stop_after" type="integer" label="Stop mapping after this number of reads have been mapped (otherwise map all)" optional="true"/>
119 <param name="mapq" type="integer" label="Samtools -q parameter" value="1"/>
120 <param name="baseq" type="integer" label="Samtools -Q parameter" value="20"/>
121 <param name="minins" type="integer" label="Bowtie 2 -I parameter. The minimum fragment length for valid paired-end alignments." value="0" >
122 <validator type="in_range" message="Must be less than -X parameter." min="0"/>
123 </param>
124 <param name="maxins" type="integer" label="Bowtie 2 -X parameter. The maximum fragment length for valid paired-end alignments." value="1000" >
125 <validator type="in_range" message="Must be greater than -I parameter." min="0"/>
126 </param>
127 </when>
128 <when value="basic"/>
129 </conditional>
130
131 </inputs>
132
133 <outputs>
134 <data format="tabular" label="SRST2 Results" name="results" from_work_dir="*.txt"/>
135 <data format="tabular" label="SRST2 Allele Scores" name="scores" from_work_dir="*.scores">
136 <filter>job_type['job'] == "mlst"</filter>
137 </data>
138 <data format="tabular" label="SRST2 Profile Scores" name="pscores" from_work_dir="*.pscores">
139 <filter> job_type['job'] == "mlst"</filter>
140 </data>
141 <data format="tabular" label="SRST2 Predicted Alleles" name="alleles" from_work_dir="*results.txt">
142 <filter> job_type['job'] == "mlst"</filter>
143 </data>
144 <data format="tabular" label="SRST2 Gene Scores" name="gscores" from_work_dir="*.scores">
145 <filter>job_type['job'] == "gene"</filter>
146 </data>
147 </outputs>
148
149 <help><![CDATA[
150
151 SRST2 - Short Read Sequence Typer (v2)
152
153 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.
154
155 ]]></help>
156
157
158 <citations>
159 <citation type="bibtex">
160 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
161 title={SRST2: Rapid genomic surveillance for public health and hospital microbiology labs},
162 url={https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0090-6},
163 journal={Genome Medicine}, publisher={BioMed Central},
164 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},
165 year={2014}, month={Nov}} ,
166 }</citation>
167 </citations>
168 </tool>