Mercurial > repos > sanbi-uwc > vcf_snps_utils

annotate intersect.xml @ 1:f8f16a682d01 draft

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author sanbi-uwc
date Thu, 16 Aug 2018 08:14:19 -0400
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1 <?xml version="1.0"?>
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2 <tool id="intersect" name="Intersect SNPs with a CSV file" version="@TOOL_VERSION@+galaxy0" profile="17.01">
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3 <description>Intersect SNPs with a CSV file</description>
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4 <macros>
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5 <import>vcf_snps_utils_macros.xml</import>
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6 </macros>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$input_vcf' data.vcf &&
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10 ln -s '$input_csv' data.csv &&
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11 vcf_snps_utils intersect data.vcf data.csv --out "$output_pdf.file.path"
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12 ]]>
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13 </command>
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15 <inputs>
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16 <param name="input_vcf" type="data" format="vcf" label="Input VCF" />
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17 <param name="input_csv" type="data" format="csv" label="Input CSV" />
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18 </inputs>
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20 <outputs>
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21 <data name="output_pdf" format="pdf" label="SNPs Intersection Report" />
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22 <data name="output_txt" format="txt" label="SNPs Intersection Combination Report" />
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23 <data name="output_r" format="R" label="SNPs Intersection R object" />
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24 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input_vcf" value="sample1.vcf" />
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29 <output name="output" compare="diff" lines_diff="2" file="sample1.html" ftype="html" />
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30 </test>
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31 </tests>
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32
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33 <help>
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35 **What it does**
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37 Intersect SNPs and generate an output report from a CSV file of knowned SNPs (workflow generated/annotated)
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39 Usage: vcf_snps_utils intersect [OPTIONS] [VCFFILES]... CSVFILE
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41 -----
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43 **Example**
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45 VCF snp intersect tool (CSV file).
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47 This tools compares CSV snps to the VCF snps This is to establish whether
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48 the discovered (VCF snps) have been discovered in the pass. This will
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49 potential be extended to include verification using other external source
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50 such as databases/api.
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52 CSV File passed should be in the following format (Example):
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53 position in H37Rv gene short name snp_type Reference Sample1 Sample2 Sample3
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54 1285 dnaA dnaA1285 nsSNP G G G G
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55 4013 recF recF4013 nsSNP T C C C
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57 Report bugs to: combattb-help@sanbi.ac.za CombatTB home page:
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58 <http://www.combattb.org/software/tools/> General help using CombatTB
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59 software: <http://www.combattb.org/gethelp/>
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61 Options:
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62 --out TEXT set the output directory, default is
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63 "/tmp/vcf_snps_utils_output/"
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64 --help Show this message and exit.
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66 vcf_snps_utils intersect example.vcf example.csv --out output/test
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67
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68 </help>
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70 </tool>