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comparison tools/naive_variant_caller.xml @ 12:ac0235d2d459 draft

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planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit ce964ed3ab7e390754fa03bb32a593fbe79dcf04
author blankenberg
date Thu, 17 Sep 2015 14:56:15 -0400
parents 8af4e7a4d041
children cfc86c3fc5c8
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11:8af4e7a4d041 12:ac0235d2d459
1 <tool id="naive_variant_caller" name="Naive Variant Caller" version="0.0.1"> 1 <tool id="naive_variant_caller" name="Naive Variant Caller" version="0.0.2">
2 <description> - tabulate variable sites from BAM datasets</description> 2 <description> - tabulate variable sites from BAM datasets</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.7.1">numpy</requirement> 4 <requirement type="package" version="1.7.1">numpy</requirement>
5 <requirement type="package" version="0.0.1">pyBamParser</requirement> 5 <requirement type="package" version="0.0.1">pyBamParser</requirement>
6 <requirement type="package" version="0.0.1">pyBamTools</requirement> 6 <requirement type="package" version="0.0.2">pyBamTools</requirement>
7 </requirements> 7 </requirements>
8 <stdio> 8 <stdio>
9 <exit_code range="1:" err_level="fatal" /> 9 <exit_code range="1:" err_level="fatal" />
10 <exit_code range=":-1" err_level="fatal" /> 10 <exit_code range=":-1" err_level="fatal" />
11 </stdio> 11 </stdio>
50 --coverage_dtype "${advanced_options.coverage_dtype}" 50 --coverage_dtype "${advanced_options.coverage_dtype}"
51 #end if 51 #end if
52 ${advanced_options.safe} 52 ${advanced_options.safe}
53 #end if 53 #end if
54 </command> 54 </command>
55 <version_command interpreter="python">naive_variant_caller.py --version</version_command>
55 <inputs> 56 <inputs>
56 <conditional name="reference_source"> 57 <conditional name="reference_source">
57 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> 58 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
58 <option value="cached">Locally cached</option> 59 <option value="cached">Locally cached</option>
59 <option value="history">History</option> 60 <option value="history">History</option>
120 </inputs> 121 </inputs>
121 <outputs> 122 <outputs>
122 <data format="vcf" name="output_vcf" /> 123 <data format="vcf" name="output_vcf" />
123 </outputs> 124 </outputs>
124 <help> 125 <help>
125 .. class:: warningmark
126
127 Upgrading to version 0.0.2 is recommended.
128
129 ------
130
131 **What it does** 126 **What it does**
132 127
133 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. 128 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.
134 129
135 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. 130 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.