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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Tue, 07 May 2019 16:01:52 -0400
parents eefdd97a6749
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jpayne@0 1 <tool id="snp-pipeline" name="CFSAN SNP Pipeline" version="1.0.1">
jpayne@0 2 <description>Build SNP table in VCF format from fastq collections</description>
jpayne@0 3 <requirements>
jpayne@0 4 <requirement type="package">bowtie2</requirement>
jpayne@0 5 <requirement type="package">smalt</requirement>
jpayne@0 6 <requirement type="package">samtools</requirement>
jpayne@0 7 <requirement type="package">picard</requirement>
jpayne@0 8 <requirement type="package">varscan</requirement>
jpayne@0 9 <requirement type="package">tabix</requirement>
jpayne@0 10 <requirement type="package">bgzip</requirement>
jpayne@0 11 <requirement type="package">fastq-dump</requirement>
jpayne@0 12 <requirement type="package">biopython</requirement>
jpayne@0 13 <requirement type="python-module">snp-pipeline</requirement>
jpayne@0 14 </requirements>
jpayne@0 15 <command detect_errors="exit_code"><![CDATA[
jpayne@0 16 cfsan_snp_pipeline $command -i <(
jpayne@0 17 $__tool_directory__/snp-wind.py
jpayne@0 18 #for $e in $fastqs
jpayne@0 19 -n $e.forward.display_name -f $e.forward.fastq -r $e.reverse.fastq
jpayne@0 20 #end for
jpayne@0 21 .
jpayne@0 22 )
jpayne@0 23 && cat ./error.log 1>&2
jpayne@0 24 && source ./snp-unwind.sh
jpayne@0 25 ]]></command>
jpayne@0 26 <configfiles>
jpayne@0 27 <configfile name="config_file">
jpayne@0 28
jpayne@0 29 </configfile>
jpayne@0 30 </configfiles>
jpayne@0 31 <inputs>
jpayne@0 32 <conditional name="reference">
jpayne@0 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">
jpayne@0 34 <option value="curated">Use a GalaxyTraker reference</option>
jpayne@0 35 <option value="history">Use a reference from your history</option>
jpayne@0 36 </param>
jpayne@0 37 <when value="curated">
jpayne@0 38 <param name="reference_fasta" type="select" label="Select reference fasta">
jpayne@0 39 <options from_data_table="all_fasta">
jpayne@0 40 <filter type="sort_by" column="2"/>
jpayne@0 41 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
jpayne@0 42 </options>
jpayne@0 43 </param>
jpayne@0 44 </when>
jpayne@0 45 <when value="history">
jpayne@0 46 <param name="reference_fasta" type="data" format="fasta" label="Select reference fasta" />
jpayne@0 47 </when>
jpayne@0 48 </conditional>
jpayne@0 49 <!--
jpayne@0 50 <param name="fa_vcf" type="select" label="Select FASTA or VCF output for consensus results">
jpayne@0 51 <option value="fa">Consensus results in FASTA format</option>
jpayne@0 52 <option value="vc">Consensus results in VCF format<option>
jpayne@0 53 </param>
jpayne@0 54 -->
jpayne@0 55 <conditional name="input_arrangement">
jpayne@0 56 <param name="inp" type="select" label="Input data layout">
jpayne@0 57 <option value="manual">Define paired collections of files from your history</option>
jpayne@0 58 <option value="collection">Use a paired-end dataset collection</option>
jpayne@0 59 </param>
jpayne@0 60 </conditional>
jpayne@0 61 <repeat name="fastqs" title="FASTQ collections">
jpayne@0 62 <param name="forward" type="data" format="fastq,fastqsanger" label="Forward reads" />
jpayne@0 63 <param name="reverse" type="data" format="fastq,fastqsanger" label="Reverse reads" />
jpayne@0 64 </repeat>
jpayne@0 65 </inputs>
jpayne@0 66
jpayne@0 67 <outputs>
jpayne@0 68 <data format="txt" label="SNP List" name="snplist" from_work_dir="snplist.txt"/>
jpayne@0 69 <!-- <conditional name="fasta_vcf"> -->
jpayne@0 70
jpayne@0 71 <data format="fasta" label="Consensus base calls" name="confasta" from_work_dir="consensus.fasta"/>
jpayne@0 72 <data format="fasta" label="Filtered consensus base calls" name="confastafil" from_work_dir="consensus.fasta"/>
jpayne@0 73 <data format="vcf" label="Consensus base calls" name="convcf" from_work_dir="consensus.vcf"/>
jpayne@0 74 <data format="vcf" label="Filtered consensus base calls" name="convcffil" from_work_dir="consensus_preserved.vcf"/>
jpayne@0 75 <!-- </conditional> -->
jpayne@0 76 <data format="fasta" label="SNP matrix" name="snpma" from_work_dir="snpma.fasta"/>
jpayne@0 77 <data format="fasta" label="Filtered SNP matrix" name="snpmalfil" from_work_dir="snpma_preserved.fasta"/>
jpayne@0 78 <data format="vcf" label="SNP matrix" name="snpmav" from_work_dir="snpma.vcf"/>
jpayne@0 79 <data format="vcf" label="Filtered SNP matrix" name="snpmavfil" from_work_dir="snpma_preserved.vcf"/>
jpayne@0 80
jpayne@0 81 <data format="tsv" label="SNP distance, pairwise" name="snpdi" from_work_dir="snp_distance_pairwise.tsv"/>
jpayne@0 82 <data format="tsv" label="Filtered SNP distance, pairwise" name="snpdifil" from_work_dir="snp_distance_pairwise_preserved.tsv"/>
jpayne@0 83 <data format="tsv" label="SNP distance matrix" name="snpdima" from_work_dir="snp_distance_matrix.tsv"/>
jpayne@0 84 <data format="tsv" label="Filtered SNP distance matrix" name="snpdimafil" from_work_dir="snp_distance_matrix_preserved.tsv"/>
jpayne@0 85 <data format="fasta" label="Reference SNPs" name="refsnp" from_work_dir="referenceSNP.fasta"/>
jpayne@0 86 <data format="fasta" label="Filtered reference SNPs" name="refsnpfil" from_work_dir="referenceSNP_preserved.fasta"/>
jpayne@0 87 <data format="tsv" label="Metrics" name="metrics" from_work_dir="metrics.tsv"/>
jpayne@0 88
jpayne@0 89
jpayne@0 90 </outputs>
jpayne@0 91 <help><![CDATA[
jpayne@0 92 <p>
jpayne@0 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.
jpayne@0 94 <p>
jpayne@0 95 The SNP Pipeline was developed by the <b>United States Food and Drug Administration, Center for Food Safety and Applied Nutrition</b>.
jpayne@0 96 <p>
jpayne@0 97 Free software.
jpayne@0 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>
jpayne@0 99 Source Code: <a target="_blank" href="https://github.com/CFSAN-Biostatistics/snp-pipeline">https://github.com/CFSAN-Biostatistics/snp-pipeline</a>
jpayne@0 100 PyPI Distribution: <a target="_blank" href="https://pypi.python.org/pypi/snp-pipeline">https://pypi.python.org/pypi/snp-pipeline</a>
jpayne@0 101 ]]></help>
jpayne@0 102 <citations>
jpayne@0 103 <citation type="doi">10.7717/peerj-cs.20</citation>
jpayne@0 104 <citation type="bibtex">
jpayne@0 105 @misc{cfsan-snp-pipeline,
jpayne@0 106 author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain},
jpayne@0 107 year = {2015},
jpayne@0 108 title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data},
jpayne@0 109 url = {https://doi.org/10.7717/peerj-cs.20},
jpayne@0 110 journal = {PeerJ Computer Science},
jpayne@0 111 }</citation>
jpayne@0 112 </citations>
jpayne@0 113 </tool>