Mercurial > repos > sanbi-uwc > vcf_snps_utils

annotate intersect.xml @ 6:51bc4a693493 draft

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planemo upload for repository https://github.com/COMBAT-TB/vcf_snps_utils commit 738f22d38aa7721ccf5fb300f0185adac948beae
author sanbi-uwc
date Mon, 20 Aug 2018 05:19:41 -0400
parents 796bf12181f6
children a074dbf35f0c
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1 <?xml version="1.0"?>
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2 <tool id="vcf_snps_utils_intersect" name="IntersectSNPs" version="@TOOL_VERSION@+galaxy0">
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3 <description>Intersect SNPs with a CSV file</description>
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4 <macros>
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5 <token name="@TOOL_VERSION@">0.0.2</token>
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6 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">vcf_snps_utils</requirement>
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10 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 ln -s '$input_vcf' data.vcf &&
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14 ln -s '$input_csv' data.csv &&
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15 vcf_snps_utils intersect data.vcf data.csv --outdir "$output_pdf.files_path" &&
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16 mv "$output_pdf.files_path"/Intervene_upset.pdf $output_pdf &&
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17 mv "$output_pdf.files_path"/Intervene_upset_combinations.txt $output_txt
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18 ]]>
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19 </command>
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21 <inputs>
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22 <param name="input_vcf" type="data" format="vcf" label="Input VCF" />
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23 <param name="input_csv" type="data" format="csv" label="Input CSV" />
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24 </inputs>
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26 <outputs>
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27 <data name="output_pdf" format="pdf" label="SNPs Intersection Report" />
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28 <data name="output_txt" format="txt" label="SNPs Intersection Combination Report" />
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29 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input_vcf" value="sample1.vcf" />
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34 <output name="output" compare="diff" lines_diff="2" file="sample1.html" ftype="html" />
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38
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39 **What it does**
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41 Intersect SNPs and generate an output report from a CSV file of knowned SNPs (workflow generated/annotated)
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43 Usage: vcf_snps_utils intersect [OPTIONS] [VCFFILES]... CSVFILE
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45 -----
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47 **Example**
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49 VCF snp intersect tool (CSV file).
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51 This tools compares CSV snps to the VCF snps This is to establish whether
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52 the discovered (VCF snps) have been discovered in the pass. This will
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53 potential be extended to include verification using other external source
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54 such as databases/api.
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56 CSV File passed should be in the following format (Example):
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57 position in H37Rv gene short name snp_type Reference Sample1 Sample2 Sample3
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58 1285 dnaA dnaA1285 nsSNP G G G G
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59 4013 recF recF4013 nsSNP T C C C
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61 Report bugs to: combattb-help@sanbi.ac.za CombatTB home page:
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62 <http://www.combattb.org/software/tools/> General help using CombatTB
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63 software: <http://www.combattb.org/gethelp/>
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64
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65 Options:
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66 --out TEXT set the output directory, default is
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67 "/tmp/vcf_snps_utils_output/"
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68 --help Show this message and exit.
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70 vcf_snps_utils intersect example.vcf example.csv --out output/test
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72 ]]></help>
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73 </tool>