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