Mercurial > repos > sanbi-uwc > vcf_snps_utils

annotate intersect.xml @ 7:a074dbf35f0c draft

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planemo upload for repository https://github.com/COMBAT-TB/vcf_snps_utils commit 443745757700041f56328d9f35343178ea48bbb9
author sanbi-uwc
date Thu, 23 Aug 2018 06:04:16 -0400
parents 51bc4a693493
children 28479a8ecb3d
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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@"><v0 class="0 3b1"></v0></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 vcf_snps_utils intersect *.vcf '$input_csv' --outdir "$output_report.files_path" &&
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14 mv vcf_intesect_report.html $output_report
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15 ]]>
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16 </command>
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18 <inputs>
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19 <param name="input_vcfs" type="data" format="vcf" label="Select Workflow VCF Datasets" min="1" multiple="True"/>
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20 <param name="input_csv" type="data" format="csv" label="Input CSV" />
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21 </inputs>
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23 <outputs>
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24 <data name="output_report" format="html" label="SNPs Intersect output report" />
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25 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input_vcfs" value="test.vcf" />
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30 <output name="output_report" compare="diff" lines_diff="2" file="report.html" ftype="html" />
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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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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68 ]]></help>
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69 </tool>