Mercurial > repos > blankenberg > naive_variant_caller

comparison naive_variant_caller.xml @ 16:07e71cf6c8ef draft

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planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
author blankenberg
date Tue, 03 Apr 2018 10:52:11 -0400
parents aff38ea879f1
children 6be51647d31a
comparison
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15:aff38ea879f1 16:07e71cf6c8ef
1 <tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.3"> 1 <tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.4">
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="0.0.3">nvc</requirement> 4 <requirement type="package" version="0.0.4">nvc</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 <exit_code range=":-1" /> 8 <exit_code range=":-1" />
9 </stdio> 9 </stdio>
101 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" /> 101 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" />
102 102
103 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" /> 103 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
104 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/> 104 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/>
105 105
106 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/> 106 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="True" label="Report counts by strand"/>
107 107
108 <conditional name="advanced_options"> 108 <conditional name="advanced_options">
109 <param name="advanced_options_selector" type="select" label="Show Advanced Options"> 109 <param name="advanced_options_selector" type="select" label="Show Advanced Options">
110 <option value="basic" selected="True">Hide Advanced Options</option> 110 <option value="basic" selected="True">Hide Advanced Options</option>
111 <option value="advanced">Show Advanced Options</option> 111 <option value="advanced">Show Advanced Options</option>
143 <param name="use_strand" value="False" /> 143 <param name="use_strand" value="False" />
144 <param name="advanced_options_selector" value="advanced" /> 144 <param name="advanced_options_selector" value="advanced" />
145 <param name="coverage_dtype" value="uint8" /> 145 <param name="coverage_dtype" value="uint8" />
146 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" /> 146 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
147 </test> 147 </test>
148 <test>
149 <param name="reference_source_selector" value="history" />
150 <param name="input_bam" value="fake_phiX174_reads_1.bam" ftype="bam" />
151 <param name="ref_file" value="phiX174.fasta" ftype="fasta" />
152 <param name="regions" value="0" />
153 <param name="min_support_depth" value="0" />
154 <param name="min_base_quality" value="" />
155 <param name="min_mapping_quality" value="" />
156 <param name="ploidy" value="2" />
157 <param name="variants_only" value="False" />
158 <param name="use_strand" value="True" />
159 <param name="advanced_options_selector" value="advanced" />
160 <param name="coverage_dtype" value="uint8" />
161 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_2.vcf" compare="contains" />
162 </test>
148 </tests> 163 </tests>
149 <help> 164 <help>
150 The **Naive Variant Caller** tool (NVC). 165 The **Naive Variant Caller** tool (NVC).
151 166
152 ------ 167 ------