comparison intersect.xml @ 7:a074dbf35f0c draft

planemo upload for repository https://github.com/COMBAT-TB/vcf_snps_utils commit 443745757700041f56328d9f35343178ea48bbb9

6:51bc4a693493

<?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**

7:a074dbf35f0c

<?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@"><v0 class="0 3b1"></v0></token>
  </macros>

   <requirements>
    <requirement type="package" version="@TOOL_VERSION@">vcf_snps_utils</requirement>
  </requirements>
        
  <command detect_errors="exit_code"><![CDATA[
    vcf_snps_utils intersect *.vcf '$input_csv' --outdir "$output_report.files_path" &&
    mv vcf_intesect_report.html $output_report
    ]]>                                                                                                                 
  </command>
        
  <inputs>
    <param name="input_vcfs" type="data" format="vcf" label="Select Workflow VCF Datasets" min="1" multiple="True"/> 
    <param name="input_csv" type="data" format="csv" label="Input CSV" />
  </inputs>
        
  <outputs>
    <data name="output_report" format="html" label="SNPs Intersect output report" />
  </outputs>
        
  <tests>
    <test>
      <param name="input_vcfs" value="test.vcf" />
      <output name="output_report" compare="diff" lines_diff="2" file="report.html" ftype="html" />
    </test>
  </tests>
  <help><![CDATA[

  **What it does**