view intersect.xml @ 6:51bc4a693493 draft

planemo upload for repository https://github.com/COMBAT-TB/vcf_snps_utils commit 738f22d38aa7721ccf5fb300f0185adac948beae

<?xml version="1.0"?> 
<tool id="vcf_snps_utils_intersect" name="IntersectSNPs" version="@TOOL_VERSION@+galaxy0">
  <description>Intersect SNPs with a CSV file</description>
  <macros>
    <token name="@TOOL_VERSION@">0.0.2</token>
  </macros>

   <requirements>
    <requirement type="package" version="@TOOL_VERSION@">vcf_snps_utils</requirement>
  </requirements>
        
  <command detect_errors="exit_code"><![CDATA[
    ln -s '$input_vcf' data.vcf &&
    ln -s '$input_csv' data.csv &&
    vcf_snps_utils intersect data.vcf data.csv --outdir "$output_pdf.files_path" &&
    mv "$output_pdf.files_path"/Intervene_upset.pdf $output_pdf &&
    mv "$output_pdf.files_path"/Intervene_upset_combinations.txt $output_txt
    ]]>                                                                                                                 
  </command>
        
  <inputs>
    <param name="input_vcf" type="data" format="vcf" label="Input VCF" />
    <param name="input_csv" type="data" format="csv" label="Input CSV" />
  </inputs>
        
  <outputs>
    <data name="output_pdf" format="pdf" label="SNPs Intersection Report" />
    <data name="output_txt" format="txt" label="SNPs Intersection Combination Report" />
  </outputs>
        
  <tests>
    <test>
      <param name="input_vcf" value="sample1.vcf" />
      <output name="output" compare="diff" lines_diff="2" file="sample1.html" ftype="html" />
    </test>
  </tests>
  <help><![CDATA[

  **What it does**

  Intersect SNPs and generate an output report from a CSV file of knowned SNPs (workflow generated/annotated)

  Usage: vcf_snps_utils intersect [OPTIONS] [VCFFILES]... CSVFILE

  -----

  **Example**

  VCF snp intersect tool (CSV file).

  This tools compares CSV snps to the VCF snps This is to establish whether
  the discovered (VCF snps) have been discovered in the pass. This will
  potential be extended to include verification using other external source
  such as databases/api.

  CSV File passed should be in the following format (Example):
  position in H37Rv        gene    short name      snp_type        Reference       Sample1   Sample2       Sample3
  1285     dnaA    dnaA1285        nsSNP   G       G       G       G
  4013     recF    recF4013        nsSNP   T       C       C       C

  Report bugs to: [e-mail] CombatTB home page:
  <http://www.combattb.org/software/tools/> General help using CombatTB
  software: <http://www.combattb.org/gethelp/>

  Options:
    --out TEXT  set the output directory, default is
              "/tmp/vcf_snps_utils_output/"
    --help      Show this message and exit.

  vcf_snps_utils intersect example.vcf example.csv --out output/test

  ]]></help>
</tool>