Mercurial > repos > sanbi-uwc > vcf_snps_utils

comparison intersect.xml @ 2:cb2055ee4e6c draft

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planemo upload for repository https://github.com/COMBAT-TB/vcf_snps_utils commit 25c750eea54d573ae0dcd3e5af23cffb8ba4c63b
author sanbi-uwc
date Thu, 16 Aug 2018 08:25:04 -0400
parents f8f16a682d01
children ec601f9af09b
comparison
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1:f8f16a682d01 2:cb2055ee4e6c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="intersect" name="Intersect SNPs with a CSV file" version="@TOOL_VERSION@+galaxy0" profile="17.01"> 2 <tool id="intersect" name="Intersect SNPs with a CSV file" version="@TOOL_VERSION@+galaxy0" profile="17.01">
3 <description>Intersect SNPs with a CSV file</description> 3 <description>Intersect SNPs with a CSV file</description>
4 <macros> 4 <macros>
5 <import>vcf_snps_utils_macros.xml</import> 5 <token name="@TOOL_VERSION@">0.0.2</token>
6 </macros> 6 </macros>
7
8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">vcf_snps_utils</requirement>
10 </requirements>
7 11
8 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_vcf' data.vcf && 13 ln -s '$input_vcf' data.vcf &&
10 ln -s '$input_csv' data.csv && 14 ln -s '$input_csv' data.csv &&
11 vcf_snps_utils intersect data.vcf data.csv --out "$output_pdf.file.path" 15 vcf_snps_utils intersect data.vcf data.csv --out "$output_pdf.file.path"
27 <test> 31 <test>
28 <param name="input_vcf" value="sample1.vcf" /> 32 <param name="input_vcf" value="sample1.vcf" />
29 <output name="output" compare="diff" lines_diff="2" file="sample1.html" ftype="html" /> 33 <output name="output" compare="diff" lines_diff="2" file="sample1.html" ftype="html" />
30 </test> 34 </test>
31 </tests> 35 </tests>
32 36
33 <help> 37 <help>
34 38
35 **What it does** 39 **What it does**
36 40
37 Intersect SNPs and generate an output report from a CSV file of knowned SNPs (workflow generated/annotated) 41 Intersect SNPs and generate an output report from a CSV file of knowned SNPs (workflow generated/annotated)