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date Wed, 24 Jan 2018 14:18:21 -0500
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1 <tool id="snp-pipeline" name="CFSAN SNP Pipeline" version="1.0.1">
2 <description>Build SNP table in VCF format from fastq collections</description>
3 <requirements>
4 <requirement type="package">bowtie2</requirement>
5 <requirement type="package">smalt</requirement>
6 <requirement type="package">samtools</requirement>
7 <requirement type="package">picard</requirement>
8 <requirement type="package">varscan</requirement>
9 <requirement type="package">tabix</requirement>
10 <requirement type="package">bgzip</requirement>
11 <requirement type="package">fastq-dump</requirement>
12 <requirement type="package">biopython</requirement>
13 <requirement type="python-module">snp-pipeline</requirement>
14 </requirements>
15 <command detect_errors="exit_code"><![CDATA[
16 cfsan_snp_pipeline $command -i <(
17 $__tool_directory__/snp-wind.py
18 #for $e in $fastqs
19 -n $e.forward.display_name -f $e.forward.fastq -r $e.reverse.fastq
20 #end for
21 .
22 )
23 && cat ./error.log 1>&2
24 && source ./snp-unwind.sh
25 ]]></command>
26 <configfiles>
27 <configfile name="config_file">
28
29 </configfile>
30 </configfiles>
31 <inputs>
32 <conditional name="reference">
33 <param name="ref" type="select" label="Use a curated GalaxyTrakr reference, or a reference from your history" help="Choose whether to use one of our references or your own from your history">
34 <option value="curated">Use a GalaxyTraker reference</option>
35 <option value="history">Use a reference from your history</option>
36 </param>
37 <when value="curated">
38 <param name="reference_fasta" type="select" label="Select reference fasta">
39 <options from_data_table="all_fasta">
40 <filter type="sort_by" column="2"/>
41 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
42 </options>
43 </param>
44 </when>
45 <when value="history">
46 <param name="reference_fasta" type="data" format="fasta" label="Select reference fasta" />
47 </when>
48 </conditional>
49 <!--
50 <param name="fa_vcf" type="select" label="Select FASTA or VCF output for consensus results">
51 <option value="fa">Consensus results in FASTA format</option>
52 <option value="vc">Consensus results in VCF format<option>
53 </param>
54 -->
55 <conditional name="input_arrangement">
56 <param name="inp" type="select" label="Input data layout">
57 <option value="manual">Define paired collections of files from your history</option>
58 <option value="collection">Use a paired-end dataset collection</option>
59 </param>
60 </conditional>
61 <repeat name="fastqs" title="FASTQ collections">
62 <param name="forward" type="data" format="fastq,fastqsanger" label="Forward reads" />
63 <param name="reverse" type="data" format="fastq,fastqsanger" label="Reverse reads" />
64 </repeat>
65 </inputs>
66
67 <outputs>
68 <data format="txt" label="SNP List" name="snplist" from_work_dir="snplist.txt"/>
69 <!-- <conditional name="fasta_vcf"> -->
70
71 <data format="fasta" label="Consensus base calls" name="confasta" from_work_dir="consensus.fasta"/>
72 <data format="fasta" label="Filtered consensus base calls" name="confastafil" from_work_dir="consensus.fasta"/>
73 <data format="vcf" label="Consensus base calls" name="convcf" from_work_dir="consensus.vcf"/>
74 <data format="vcf" label="Filtered consensus base calls" name="convcffil" from_work_dir="consensus_preserved.vcf"/>
75 <!-- </conditional> -->
76 <data format="fasta" label="SNP matrix" name="snpma" from_work_dir="snpma.fasta"/>
77 <data format="fasta" label="Filtered SNP matrix" name="snpmalfil" from_work_dir="snpma_preserved.fasta"/>
78 <data format="vcf" label="SNP matrix" name="snpmav" from_work_dir="snpma.vcf"/>
79 <data format="vcf" label="Filtered SNP matrix" name="snpmavfil" from_work_dir="snpma_preserved.vcf"/>
80
81 <data format="tsv" label="SNP distance, pairwise" name="snpdi" from_work_dir="snp_distance_pairwise.tsv"/>
82 <data format="tsv" label="Filtered SNP distance, pairwise" name="snpdifil" from_work_dir="snp_distance_pairwise_preserved.tsv"/>
83 <data format="tsv" label="SNP distance matrix" name="snpdima" from_work_dir="snp_distance_matrix.tsv"/>
84 <data format="tsv" label="Filtered SNP distance matrix" name="snpdimafil" from_work_dir="snp_distance_matrix_preserved.tsv"/>
85 <data format="fasta" label="Reference SNPs" name="refsnp" from_work_dir="referenceSNP.fasta"/>
86 <data format="fasta" label="Filtered reference SNPs" name="refsnpfil" from_work_dir="referenceSNP_preserved.fasta"/>
87 <data format="tsv" label="Metrics" name="metrics" from_work_dir="metrics.tsv"/>
88
89
90 </outputs>
91 <help><![CDATA[
92 <p>
93 The <b>CFSAN SNP Pipeline</b> is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
94 <p>
95 The SNP Pipeline was developed by the <b>United States Food and Drug Administration, Center for Food Safety and Applied Nutrition</b>.
96 <p>
97 Free software.
98 Documentation: <a target="_blank" href="http://snp-pipeline.readthedocs.io/en/latest/readme.html">http://snp-pipeline.readthedocs.io/en/latest/readme.html</a>
99 Source Code: <a target="_blank" href="https://github.com/CFSAN-Biostatistics/snp-pipeline">https://github.com/CFSAN-Biostatistics/snp-pipeline</a>
100 PyPI Distribution: <a target="_blank" href="https://pypi.python.org/pypi/snp-pipeline">https://pypi.python.org/pypi/snp-pipeline</a>
101 ]]></help>
102 <citations>
103 <citation type="doi">10.7717/peerj-cs.20</citation>
104 <citation type="bibtex">
105 @misc{cfsan-snp-pipeline,
106 author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain},
107 year = {2015},
108 title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data},
109 url = {https://doi.org/10.7717/peerj-cs.20},
110 journal = {PeerJ Computer Science},
111 }</citation>
112 </citations>
113 </tool>