comparison naive_variant_caller.xml @ 15:aff38ea879f1 draft

planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit dfca863a9a361877d6d98b92072f1ebc316c5767

14:5c852eca82e0

<tool id="naive_variant_caller" name="Naive Variant Caller" version="0.0.3">
  <description> - tabulate variable sites from BAM datasets</description>
  <requirements>
    <requirement type="package" version="0.0.3">nvc</requirement>
  </requirements>
  <stdio>

          <param name="coverage_dtype" value="uint8" />
          <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
      </test>
  </tests>
  <help>
**What it does**

This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples. 

User configurable options allow filtering reads that do not pass mapping or base quality thresholds and minimum per base read depth; user's can also specify the ploidy and whether to consider each strand separately. 

15:aff38ea879f1

<tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.3">
  <description> - tabulate variable sites from BAM datasets</description>
  <requirements>
    <requirement type="package" version="0.0.3">nvc</requirement>
  </requirements>
  <stdio>

          <param name="coverage_dtype" value="uint8" />
          <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
      </test>
  </tests>
  <help>
The **Naive Variant Caller** tool (NVC).

------

**What it does**

This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples. 

User configurable options allow filtering reads that do not pass mapping or base quality thresholds and minimum per base read depth; user's can also specify the ploidy and whether to consider each strand separately.