comparison tools/naive_variant_caller.xml @ 12:ac0235d2d459 draft

planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit ce964ed3ab7e390754fa03bb32a593fbe79dcf04

11:8af4e7a4d041

<tool id="naive_variant_caller" name="Naive Variant Caller" version="0.0.1">
  <description> - tabulate variable sites from BAM datasets</description>
  <requirements>
    <requirement type="package" version="1.7.1">numpy</requirement>
    <requirement type="package" version="0.0.1">pyBamParser</requirement>
    <requirement type="package" version="0.0.1">pyBamTools</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" err_level="fatal" />
    <exit_code range=":-1" err_level="fatal" />
  </stdio>

             --coverage_dtype "${advanced_options.coverage_dtype}"
         #end if
         ${advanced_options.safe}
     #end if 
  </command>
  <inputs>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>

  </inputs>
  <outputs>
    <data format="vcf" name="output_vcf" />
  </outputs>
  <help>
.. class:: warningmark

Upgrading to version 0.0.2 is recommended.

------

**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. 

12:ac0235d2d459

<tool id="naive_variant_caller" name="Naive Variant Caller" version="0.0.2">
  <description> - tabulate variable sites from BAM datasets</description>
  <requirements>
    <requirement type="package" version="1.7.1">numpy</requirement>
    <requirement type="package" version="0.0.1">pyBamParser</requirement>
    <requirement type="package" version="0.0.2">pyBamTools</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" err_level="fatal" />
    <exit_code range=":-1" err_level="fatal" />
  </stdio>

             --coverage_dtype "${advanced_options.coverage_dtype}"
         #end if
         ${advanced_options.safe}
     #end if 
  </command>
  <version_command interpreter="python">naive_variant_caller.py --version</version_command>
  <inputs>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>

  </inputs>
  <outputs>
    <data format="vcf" name="output_vcf" />
  </outputs>
  <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.